I've been through the same "pain" but after a few times of trying to find the best way, here's what I now always do to help align the window mask before painting:
1. Cut-up the window mask down to the shape of the window mask
2. Peel off a small part (maybe about a fifth of the whole sticker) and fold the non-adhesive backing onto itself
3. Align the mask by pressing the unpeeled part into the window while taking special care that the sticky unpeeled part of the mask doesn't stick into the window.
4. When I am satisfied that the mask is aligned to my liking, I press the sticky unpeeled part on the window, double check, and then unpeel and slowly stick on the rest.
Hope this helps.