Im currently building a guitar and im thinking of using a humbucker for the bridge pickup and a hotrail for the neck pickup. My question is can i use any pickup or are there specific types for each position? ive noticed there are some which are sold as bridge or neck pickups on ebay so i want to make sure im not buying the wrong ones.

Also im going to build my own scratch plate, would a 2mm acrylic sheet do the job without causing much loss to sound quality?

Depends what style of body you are using.
2mm acrylic should work fine

Normally the hotter pickups go in the bridge but you can do whatever you like.