I can never manage to cut the vinyl perpendicular to the roll, so to try and align the vinyl based on the cut edge would go horribly wrong for me.
If it's bunching, then either you've got too much pressure/force going on and it's cutting through or applying so much force that it's dragging. Also, check your pinch rollers and make sure that they're clean.
If you're cutting directly off of a roll, it's rolled pretty darn straight with equal tension. I rarely need to jog the vinyl back and forth to check for straight.
If it's a smaller piece, or something that isn't on a roll for me, then yes, I do jog the vinyl back and forth and gauge the 'straightness' based on the vertical (molded) lines on the front of the machine.