Gary-
You're on the right track with how the guard is formed, just watch out for some of the terminology of rank vs. file. Ranks run laterally and are one behind the other (front/rear). Files run vertically (that is if you are looking down at them in a diagram that is drawn out), and each file would contain a man from the front rank and a man from the rear rank. Picture that the following numbers are actually men in line of battle. The ranks would be the groups of men from 1-9, front on top, and rear on bottom. Files would be the matching numbers from each rank (both 1's in this example are the same file, both 2's are the same file but not the same file as the 1's, and so on). Here is one more thing that might not come up for a while, but might as well mention it now...Comrades in Arms. This is a specific term that deals with men in very small sections that work with each other in skirmishing formations, and also for stacking arms (we may get into stack for the guard and color company later, but that is a whole different beast). Comrades in Arms are groups of 4 men from both ranks. So by the numbers below, 1's & 2's are a set of Comrades in Arms, 3's & 4's are another set, 5's & 6's, 7's & 8's...9's are a set by themselves, though not the normal size of 4 men (they will be treated differently in different conditions).
987654321
987654321
Now for what I have mentioned above, the guard is different since if it is composed of 9 men, then it has 3 ranks and 3 files. For the diagram below 1-8 are the corporals (I have not numbered based on seniority, which may or may not matter), and C = Color Sergeant (based on a battalion only carrying one color).
So in this case the ranks are Front = 2C1 Middle = 543 Rear = 876
The files are 1st File = 136 2nd = C47 3rd = 258
2C1
543
876
As far as companies being compensated for the men given up to the color guard...I have never seen any cases where men will be detailed to fill in those gaps numerically. So let's say a company loses a Sgt. and a Cpl. to the guard...now maybe that company is at say 75 men...I've never seen 2 men added to that company to make up for this loss. If we wanted to compensate, how would we/where would we pull the other men from? Every other man in the regiment is already assigned somewhere in theory. Now think that every company has men that are simply not with them (desertions, sick, detailed to other areas in the army and sometimes away from the army, recruiting, etc...). The loss of 1 or 2 men to the guard (which is not really a loss since at least these men are still in line of battle) is not something that you really can or would compensate for.
Now within the company that the Sgt. and Cpl. were detailed from someone will most likely be promoted to fill the rank of Sgt. and Cpl., but from the men already in the company. If a regiment is greatly reduced in size (like most regiments from both sides after the first year or so of war), then you may see the number of NCO's carried on the rolls be reduced (i.e. you don't need 5 Sgt's and 8 Cpl's if your company is down to 20 men total). At this point there is really no patter or what/how many NCO's a company will carry, so you will need to look on a case by case basis. An example I have have data for from my own relative's unit (Co. A 30th Massachusetts Veteran Volunteers) is as follows. For the period of March-April 1864, of about 65 men Aggregate, only 35 are present for duty. Of the Aggregate there are still 5 Sgt.'s and 8 Cpl.'s, but present for duty with the company there are actually only 3 Sgt.'s and 5 Cpl.'s. At other times it dips even lower, and once in a blue moon all of the NCO's are present for duty. Note that the color company has the same allotment of NCO's as every other company in the battalion. While the guard is attached to the color company, its men are considered completely separate in almost every scenario that you can imagine. The one area where they merge (for lack of a better term), is with respect to the 2nd Sgt.'s (of the color company) position within line of battle. I believe the article by Mr. Woodard covers this, but I might be thinking of an older article from the early 90's. Normally the 2nd Sgt. of a company posts in the line of file closers (3rd rank), behind the left file of that company. In the case of the color company (since the guard is attached and lengthens the line), the 2nd Sgt. posts behind the left file of the guard (now equal to being the 4th rank). There are reasons for this, but they are complex, and go back as far as some manuals in the early/mid 1700's from when they first evolve this pattern. In the picture below * = 2nd Sgt. This picture ignores the positions of the other Sgt.'s in the company's line.
Normal Company
--------------------------------------
--------------------------------------
*
Color Company
2C1----------------------------------
543----------------------------------
876
*
So for the scenarios you have mentioned, Case 2 (separate NCO's from the guard) is correct. The reason for so many NCO's is to have the experienced men where they need to be for maneuvers...usually where there are section breaks (between companies, platoons, and sections) where battalions and companies may be broken into smaller pieces (usually by wheeling into the separate groups. In this picture of a company the #'s will represent the Cpl.'s
Normal Company
8----------76----------54----------32----------1
--------------------------------------------------
<---4th---><---3rd---><---2nd---><---1st---> (Section breaks)
<----------2nd--------><-----------1st--------> (Platoon breaks)
This gives you Cpl.'s all along the front rank at every interval where you might wheel the company into different formations.
I think this has answered the questions...now for the case study.
These details come from the 30th Massachusetts Veteran Volunteer Infantry as reported in an account available here: http://books.google.com/books?id=KIYvAAAAYAAJ&printsec=frontcover#v=onepage&q&f=false
After reading roster and service records for all the men listed below, I can say that only 2 of them were ever listed as carrying colors or serving with the guard. The listing given does not say who was in the guard at a given time, it is a composite list for the duration. At a glance you can easily see that some companies are over/under represented in members chosen for the guard.
*Note that I have had to change the format slightly to have the list work here.
"The following are the names of the Sergeants and Corporals of the color-guard of the 30th Regiment of Massachusetts --so far as can now be recalled:--
Sergeant Henry C. Brooks Co. C
" Francis Shattuck Co. D wounded at Port Hudson
" Calvin Perkins Co. A
Corporal Martin Smith (2d) Co. G
" Patrick Tobin Co. D
" William Roberts Co. C
" Wm. H Rogers Co. K lost arm at Port Hudson
" Ruel W. Greenleaf Co. C killed at Cox's Plantation
" Horace F. Davis Co. E
" Francis Houghton Co. I
" John Delaney Co. F
" Owen Gallagher Co. F
" James F. Carroll Co. H
" Jeremiah Hendley Co. H
" James Sands Co. H
" Ira B. Dennett Co. G
" Eugene M. Deering Co. C
" J.F. Dow Co. I
" Jacob Ourish Co. I
" Nathaniel R. Cole Co. I
" Walker Clapp Co. I
" Michael Donahue Co. A
" James Coulter Co. I"
So for this list our totals are:
Cpl.'s = 20 (Rogers is listed in service records as "Actg Color Corporal").
Sgt.'s = 3 (in his service records and other accounts Shattuck is listed as "Color-Sergeant", Brooks is listed as "Color-Sergeant" by his fellow soldiers, and Perkins is only ever referred to as Sgt.).
Company Breakdown (number of men in guard from a given company):
A=2 B=0 C=4 D=2 E=1 F=2 G=2 H=3 I=6 K=1
You can see that some companies are called upon more heavily for men for the guard than others. Now this is only one case, but I believe you might see similar patterns in other regiments as well.
I think that's about all that I have time to post this evening, but since I have mentioned the 30th Massachusetts (and I should be doing a large post on their colors and guard on my blog soon), and since this group loves more information relating to colors, I should share the following bit of information.
When this regiment was formed, one of its officers was Captain Timothy A. Crowley, had previous service in the 6th Massachusetts Infantry when it was under attack from a mob in the Baltimore Riot of 1861. Crowley is noteworthy because during that action he was wounded while acting as Color-Sergeant, carrying the National Colors. Here are 2 good links that describe that action.
http://www.mass.gov/portal/government-taxes/laws/interactive-state-house/key-events/battle-flag-the-minutemen-of-61.html
http://stonehamhistory.webs.com/BaltimoreRiot/MarchOf6th.htm