1. No, you can only ever install one at a time (but you can get them to install one after the other - check the options in FBI there should be a button for it). Get freeShop if you don't have it already. You don't need a special CIAs folder, you can put them on the root and delete them after installation (use Y to install [I think - double check in the program] and it will delete after installation automatically).
2. Yes, if you use Luma3DS (you may have to select region free in the options - hold Select on boot up to access the options).
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Use Luma3DS, and check updated sysNAND in the options and uncheck boot emuNAND (hold Select on boot to access options).