i was painting my guitar and took the pickups out by cutting the wires that connected them to the pots/ jack

when i put them back together i soldered the little wires that were inside the big wires together, and the bare wires together. that didnt work, so i looked on seymour duncan and their pickups have wires that my pickups dont have...im using an epiphone les paul special and the only wires are a small red wire (which i assume is hot?) and the bare wire around it
Well now you know not to cut wires! Simply desolder the things in future.

So there is one shielded wire coming from the pickup? With the hot wire isnside and a metal braid around it? If so, you have to solder the repsective wires back together. I'm guessing the problem with your wires are that you soldered them back together, but didn't stop the two shorting. Solder the two parts of the red wire together, wrap the joint with a bit of insulation tape and then solder the braid over it.