Generally speaking the only emulators that work with zip files are mame and FBA.the rest will need to be unzipped.if you configured your controllers with the retroarch config tool in the set up script and they still aren’t working it might be good to check and make sure your the folders you placed your ROMs in are utilising retroarch cores. If they aren’t they may have their own separate configs (I.e. GBA, FBA, mame, mupen64plus, etc.) I’ve made a few videos on youtube going step by step on what I did when I set up my pi, but my controllers may be different than yours- floob has some good videos that are much more thorough than mine which may be useful to you.