What CFW are you using?
If the NAND you backed up is clean and made before hacking, you should restore it before you make the EmuNAND partition. If there is any save data if you want to keep, you should back it up now so you can inject it into the EmuNAND partition later. Then just install the EmuNAND to wherever you want. There is no "best" EmuNAND solution as all 3 have their own pros and cons.
exFAT can and will corrupt, this is not up for debate. Just because it hasn't happened to you doesn't mean it will. Now that doesn't mean corruption is the end of the world as a simple format will fix that. But if you have a lot of stuff on your SD card, then its not going to be so simple. Personally FAT32 is objectively better and since you have to patch exFAT onto every firmware you install, exFAT can be quite an inconvenience.
There's really no reason to buy more than one SX Pro because although the license is embedded into the dongle, it can still send the payload for any console running SX OS. Your best bet is to simply buy a license for the second console. Also you don't "install" SX OS
Is your SD card formatted to exFAT?
There is no ETA on when those will become available nor what is and isn't possible with the unreleased exploit. You're honestly better off either returning that console for an unpatched unit or buying a second one that is unpatched, preferably used.