Ahh ok. Well you don't need to have separate installs to begin with.
If you are having troubles with certain systems, first make sure you have the cores downloaded. Second, make sure you have the correct bios files for those systems in the \Retroarch\system\ folder. You will have to find bios yourself, we cannot help you get those unfortunately. Third make sure your command line parameters are setup properly in the emulator settings window.
Stretched video is taken care of by settings in the video section, if you want stretched the aspect ratio will be set to 16:9, if you want the proper aspect ratio set it to 4:3 or core provided.
For Snes cores which one you use will depend a bit upon your system and what it can handle but I would recommend either Snes9x or BSnes Balanced Mercury to start with.
For arcade stuff I recommend sticking to a stand alone version of Mame and not using the Retroarch Mame core. FBA is fine if you want to use it for NeoGeo but it's no better or worse than Mame.