I believe you are speaking of the attack on a group of Pins, some in Federal uniform, at Manus', ten miles west of Watie's camp along the line.
Watie had about a battalion with him (all he could arm and mount), the remainder of the regiment was in camp at Webbers Falls. He was joined by some Choctaw and a few of Bryan's Cherokee Battalion from Ft Coffee -- all that Cooper could provide. I think the rest of Bryan's Battalion was scouting with Marmaduke.
I believe this combined force of about 500-600 men was the extent of what Cooper could provide in response to Hindman's orders to send all available troops north. I believe this order from Hindman leads persons to incorrectly believe Cooper's entire command was at Prairie Grove. I think this force with Watie *WAS* all of Cooper's available force at the time -- all that were armed, mounted, clothed, fed, and near enough to respond. The rest of Watie's Regiment that was left behind at Webbers Falls barely had enough percussion caps to send out scouts.
Watie was supposed to be guarding Hindman's left, which he did but he never could connect with Hindman's left flank which was on the move the entire time. After Prairie Grove, Watie learned that Hindman was falling back to the Arkansas so he began to fall back but took a side trip to Manus' and attacked a group of Pins that he heard were planning to attack him. The Pins were scattered into the hills. Watie retraced his route back to Paden's Springs (on the northwest end of Muskrat Mtn about 4 miles WSW of Evansville AR), then to Dwight Mission, and then to his regimental camp at Webbers Falls.
What was the question? Oh yeah. Like Steve said, I think they scattered "here, there, and everywhere" but it depends on the time period.
From Oct 1861 to Jul 1862, most of the Pins are at home. There may be a couple of hundred in Kansas with the Loyal Creeks et al but about 90% of Drew's Regiment are Pins and "Confederates". There was a lot of violence, revenge killings and the like, between the Treaty Party and the Ross Party but generally Watie and Drew are on the same side (gotta keep 'em separated).
Immediately after Drew's regiment defects, the white troops abandon the Indian Home Guard so the IHG has to move north and the Pin families have to go too! Eventually you have the families of the Cherokee in the IHG (half the 2nd and all the 3rd) in southern Kansas -- except for those brave souls that stayed in the Cherokee Nation.
The 3rd IHG with their refugee families are moved to Neosho MO. The three IHG regiments are assigned to separate brigades at the Battle of Prairie Grove but are subsequently combined into the Union Indian Brigade with Col Wm. A. Phillips in charge. Phillips ultimately moves back into the Cherokee Nation and tries to re-settle the Pins but Watie's raids through the Nation drive the Pin families to Ft Gibson for protection -- a huge drain on military supplies.
Many Pin families remain around Ft Gibson for the remainder of the war but eventually they begin to spread out to farm etc and as Phillips controls the crossings on the Arkansas near and below Ft Gibson, it gets much safer for Pins in the eastern Cherokee Nation -- east of the Grand/Neosho River.
So, I don't think significant numbers of Pins scattered to and remained in Kansas, Missouri, or Arkansas. The Pins didn't "mix well" with whites. The Pins didn't like or trust the whites and the Pins wore warpaint and looked too much like the "wild tribes". The Pin refugees were dependent on the US Army for subsistence. So, the Pins tend to stay together and returned to the Nation together when they could. Many had stayed in the Nation -- Wiley Britton remarks on the family reunions when Phillips marches the IHG (with their refugee families following) into Tahlequah in May 1863.
I don't know that that answers the question but I had fun typing it! As always, folks will correct me where I have mis-spoke or where they disagree with my conclusions.