If the nands are linked (using the same ID, which happens by default since the emuNand is a complete copy of sysNand), then installed CIAs will show up as "new" every time you boot, causing you to have to "unwrap" them. The sysNand will see the installed CIAs as garbage/junk data because it fails the signature check, so if you go into Data Management, it'll clear it out and delete it without any warning. I personally recommend unlinking them, but there are more guides on the subject. I believe having them linked allows you to do a couple things you can't do once they're unlinked, but I don't know the details.
CIAs can be installed without modification, but most will require the signature check to be disabled, and as such will only run in Gateway Mode. Normally, software downloaded through the eShop is signed with a key specific to your system. CIAs installed will lack that key, though. (There is a subset known as "Universal" or "Legit" that uses a universal key, software that comes pre-installed on certain systems will have this trait, and as such can run without signature checks disabled. CIAs you personally make from legitimately-purchased software you've downloaded will have a valid signature as well, though it won't work for anyone else.)
The emuNand resides on a partition that isn't visible in Explorer, because Windows doesn't know how to read and write to it. The easiest way that I know of is to use the emuNand Tool to back up your emuNand, use the Gateway Launcher to format/setup emuNand on the new card, then use the emuNand Tool to inject the backup onto the new card. Then drag and drop all the files from the old card's FAT32 partition to the new card's, and you should be good to go. That's what I did for my own card, and it worked perfectly.
