hi brinse, and welcome to
RP.
what i generally do on these is, put all the pieces in the scanner at the same time in generally the right positions. it doesnt have to be exact and they dont have to overlay or anything... just sort of close and sort of in the right order and proximity. i'll fix all that in paint shop pro. i just want a really good scan of the pieces, no matter how they're going to fit together later.
and you certainly can use a camera if you have one, but i wouldnt cover the pieces with glass... too much chance of an errant light reflection. but, if they're curved or curling or bent or something like then, then i suppose you could cover with something transparent. just be careful of reflections and bright spots.
and there are some folks here that prefer to do their 'scanning' with a digital camera rather than a scanner and may show up to help you even more than i can here. you might look around in the various forums for topics on this. i know some exist.
most scanners, at least those produced in the last few years, are going to give you a pretty good resolution, so that would be my first choice. besides, i dont have a digital camera with enough resolution right now to use it as a scanner.