Overwriting Grand Theft Auto: San Andreas mods?

Hi, I just bought Grand Theft Auto: San Andreas on the PC after it was on sale on Steam. I downgraded the client to v2 and I'm having a blast with the mods, though, how would you keep two mods? I downloaded the fuel mod, replaced the files with it's files, and it worked. Then I installed the allinone pack mod which replaces the same files the fuel mod does. It works, but now the fuel mod is gone. My question is, how can you keep multiple mods which replace the same files at once?