If i would use Ipac2 in keyboard mode is this better for the Retropie experience?

Not necessarily.

I choosed the gamepad mode for the configuration under Emulationstation for two players . Because in keyboard mode is only one player input configuration is possible (but Keyboard mode functioning under PPSSPP awesome). I know under Retroarch I have a possibility to configure a second player input too.

Yes, you can configure a 2nd player for a keyboard device, but that can't be done from EmulationStation and you'll need to edit the configuration files (retroarch.cfg). RetroArch expects mostly a gamepad since it started as a console oriented front-end emulator.

I don't really understood configuring inputs under Emulationstation , is this for the standalone emulators or just for the controlling / steering the Emulationstation. Retroarch is for the Libretro emulators input configuration ( I hope this is right ?)

Configuring the inputs in EmulationStation will auto-configure them also for RetroArch and a few other standalone emulators (Mupen64Plus/Daphne/OpenMSX). Any libretro based core should have a configuration ready once you've done it in EmulationStation.

This is getting off-topic here, if you have some more input related questions, I suggest starting a separate topic and reference your posts from here.

psp and .pbp files