IIRC, it doesn't support arguments yet, so no folder or control options are saved yet.
HOWEVER, you can have your roms in an appropriately named folder and they be quickly accessed.
For example, i have fba and neo geo games in a folder called =ARCADE= and SNES in a folder called =SNES= and GBA, GBC, TG16 CD etc in subfolders in=RETRO=.
This way, they are at the top of the file browser list AND when i want to use SNES9XGX, GenPlusGX and mednafen, they auto load them from there,after i configured those three emus.
That's just me though, i use RA for fba and TGCD and some SNES. You can experiment renaming and folder structure, based on what emus you use for each retro console.
After the performance enhancement and compatibility improvement of course, arguments and memory leakage fix in order to prevent stack dumps are the only things to perfectionize this great emu