You should create an emummc (emulated copy of your Switch internal memory - sysmmc). Then you use sysmmc for you official games and emummc for your unofficial games and homebrew. That way you can play the games you bought online in sysmmc, keeping it clean. Make sure emummc is either offline or use DNSmitm to block Nintendo servers. Otherwise you might get banned by Nintendo which will affect both emummc and sysmmc.
You are correct that If you don't enter rcm when you turn on your Switch then cfw will not be activated and you will end up in sysmmc. If you enter rcm you can choose between sysmmc or emummc depending on which payload and which config you use.
So yes you will be able to play online but only your officially bought games in sysmmc
Yes you can access you downloaded games in emummc but only offline