Do you have the CDI's for King of Fighters XI and NeoGeo Battle Coliseum? Those are the only Atomiswave games I am currently missing.All those working here from USB except I haven't tried psp. My sega dreamcast games are in .chd format.
I found PPSSPP Standalone to be much more forgiving than RetroArch when it comes to setting up your PSP Library. I did manage to get FlyCast Core to boot my DC Games (Hokuto No Ken, Capcom VS SNK 2 & Marvel VS Capcom 2 just to name a few) within RetroArch by brute forcing my BIO's setup (extracting everything to a Root Folder as well as sorting them via Folders per Platform.
While the convenience of RetroArch being the All-In-One IS enticing , I've come to terms that most of the Standalone Apps (FlyCast, PPSSPP, XSXPS2) are much more user friendly and far less intimidating when it comes to setting up everything in app.