I like to space the baffles a little tighter, about 5" between them. 6" would probably be fine.
If you're shooting for 3" of loft, then you probably want to cut a 3" strip of netting for each baffle. When sewn in that'll be closer to 2.5" or so, which should help maximize density/minimize cold spots while allowing great loft. Cut the 3" strip for the overall width of your fabric at that point... so for your topmost baffle, cut it at 48" long.