the pcsx-reArmed emulator supplied with retropie is a fairly ‘pure’ experience, and doesn’t let you do too much with the graphics. other than the ‘enhanced resolution’ setting you’ve already found. i found that option alone added sound distortion, so you might find performance hitches with it turned on. also, it didn’t appear to make any improvement to games which already run in the PS1’s “high” resolution mode (eg, Tekken 3). i suppose it just forces that mode on games that don’t use it?
for filters, there’s so many that it’s difficult to recommend one. almost all of them will crush your framerate. i use the ‘dotmask’ filter, but it’s a very subtle effect, more about authenticity than anything else. you might want a scanline overlay (see the various threads of this), but again, more of authenticity thing.
to save your settings: Frontend Settings > Configuration Settings > Save Config on exit to ON (this saves to the config when we exit the game – might want to turn this off later, in case you mess anything up later by accident)