Hints on putting neoprene over shoes on (this is how I do it, YMMV):
1) put toe in the front, then pull this as snug as possible by pulling on the cleat hole.
2) then grab the back of the heel hole below the zip and stretch this over your heel
3) then pull on the zip and top to get the whole thing fitting snug, then do the zip up.
I have size 43/44 road shoes and they're a nice snug fit. They just go over my 44 recessed MTB shoes though.
One thing to avoid is pulling on the neoprene itself, as this can cause it to rip, especially the folds that you get on both sides after stage 1.
Repair: I've used rubber shoe type glues (Total Glue, shoe goo) which work well and are cheaper but not quite as good as neoprene glue (Black witch). Vinyl glue (151) does stick neoprene but isn't quite flexible enough for all areas. Rubber Vulcanising Solution (out of your puncture repair kit) will also stick neoprene. I've also got repair patches on the insides of both ankles where they rub the cranks (like the circle on converse trainers) stuck on exactly the same way as repairing a puncture. I've had a few crashes with my current pair and managed to keep them going.
I find it's the main seam at the front where it flexs on each pedal stroke that gradually deteriorates with horizontal cracks, beyond my ability to glue it.
Edit: my instructions are for the endura or bbb types with two holes in the sole, the ones with a velcro strap might be different, I've not used them.