I put my BL starters in at the beginning. Set player rest to hook 'em after the 4th inning or so. (I use player rest and defensive replacements all the time, try to use as many players per game as I can, don't want to see anyone getting five or six ABs unless it's intentional.)
Let the BL SPs have the first five games, then park them in rest. After three or four games... about 10 ABs... I move the position players to rest. Then the minor leaguers play out the majority of the ex schedule, especially ones who I want to see projected in certain roles.
With three or four games to go I start bringing the big leaguers back in to finish up the sked and get some dress rehearsal. Try to end up with pretty much the numbers Mike says.