I just align the wheel, push it down to cut through, then drag it along the desired line. As long as the original line-up is done carefully, this gives me nice clean cuts.

I also cover the area with 2" wide masking tape first, then mark the cut-lines on that. This gives some basic protection to the fibreglass in case the chuck of the (Dremel / Minicraft / whatever) rubs against the glasswork because I'm focusing intently on the cutting disk instead of the chuck.