Make sure you've got the boots that match your calipers. It's been a long time (I love DOT 5) but ISTR I put the boot on the piston first, with the lip hanging over the edge just far enough to reach the groove inside the caliper bore, then twisted the piston & boot until the lip laid smooth. After that, it's just a matter of pushing the piston in without letting it get cocked. If it starts to cock, you may be able to pry or clamp against the opposite edge to straighten it out, or you may have to force it back out and start over.