I've been doing a lot of this sort of thing lately, so here's my 2 cents on the issue (hey, I just noticed for the first time that there's no "cent-symbol" on a keyboard. But anyway...)
When I draw ROIS, I find it much more reassuring to draw them directly on the EPI image. It's really surprising how poor the resolution of these is if you're used to looking at interpolated functional maps overlaid on anatomical images. It's easy to do this kind of drawing in AFNI. Just open two windows "locked together." In one, draw the ROI on top of your EPI image, and in the other have the coregistered anatomical image with the ROI dataset (currently being drawn) set as the functional overlay. That way, you get to control directly which voxels are chosen, while at the same time seeing them appear (as disturbingly large chunks!) on the anatomical image, and it's not any more effort than drawing on the anatomicals.
-Jed