Are you installing the "hook" side of the clips first? (meaning the rearward, outward side first). I start by folding the boot in half, (finish top to finish top), lay it over half the well, and start with the middle rear clip. I reach one hand under the boot to help guide while 'hooking' the first clip on, then snapping the longer piece downward with pressure over the top of the boot. Then work your way along the rest of that rear edge. Then I jump over to the other rear edge after gently folding the boot over that way. If you are slightly off center, now you can gently tug or push the clips along the chrome to adjust left or right and tightening to get rid of as many wrinkles as possible. Then do the sides and the interior snaps last. Then you have to go back and tuck the front of the boot edge behind the seat frame. Believe me, if the boot is not TIGHT, it will lift and blow in a stiff cross wind. To remove the boot, do the same in reverse. You need to reach your hand under the boot to pop the clips upward from underneath, then remove the "hook" portion as you go.
I will admit it is a PITA, but it looks so much nicer with the boot on.

And I agree with OHC, do NOT switch to snaps. You will devalue your car a couple thousand bucks doing that.