Hi vincent,
First you must ask yourself some issues:
1.- will All moodles share the same courses ?
2.- The think will change betwen them will be only themes ?
If you awnser yes the two question, you can do it with minor changes, but if you say no, them the best option will be install it in differents databases or use others prefix. like: mdl1_, mdl2_, mdl3_,...,mdln_
The 'yes' option requires diferent theme records in config table, and in the theme function.
I hope you find this helpfull, and if you resolve this with a diferent option please post it because a lot of people try in some point to do it.
N.B.