I have downloaded SimPE to recolour some custom paintings for a project. I found the images I wanted to use, exported the recolour texture to photoshop after i had cloned it from the original, and spent ages creating the recolours. Thing is, when I started the game, the recolours are not there. Is there something I have done wrong, does each texture need it's own name?

Yes each texture needs its own name. You need to run object workshop > recolor option for each recolor. You also should *not* use the clone option if your only recoloring a painting. Cloning is for when you want to change the mesh somehow.