Bonnie --

Unlike many, once the fighting ended, Gaines Mill was a battlefield occupied by the Confederates. As for treatment of the dead of both sides, here's a note from a report by Col. J. Foster Marshall, First South Carolina Rifles. He describes the work which occupied his men the day following this battle:

Early that morning I made a detail from each company to bury the dead, and so severe was the work of death in some of the companies that it took the detail all day to bury their dead. This sad duty performed, we were permitted again to sleep that night on the battlefield.

[Official Records, Ser. I, Vol. XI/2, p. 874]

The standard, time-honored practice of the armies was to inter those who died in battle on the field itself. You may contact the National Park Service at Richmond for further particulars about disposition of Confederate dead from the Seven Days' Battles.

http://www.nps.gov/rich/pphtml/maps.html

Pictured below is the cover for Mr. Coco's study of Confederate dead on the Gettysburg battlefield. His image of a shallow grave for several soldiers and their crude wooden markers serves to illustrate how most of the dead were buried.

Dead of the 5th North Carolina and other unfortunate North Carolina boys of Iverson's Brigade were buried in a mass grave near where they died. Afterwards a farmer planted a vineyard here. Grapes grown in the soil over this burial trench were processed and sold to visitors as "battlefield wine".