If the two are linked, then they'll be trying to use the same folder, and getting confused. One symptom is that installed CIAs are seen as "new" every time, so you constantly have to unwrap them. Another is that themes and certain settings from one nand carry over to the other (like setting colors and such), which can make it hard to distinguish which nand you're running. Also, if they're running different versions, there's a good chance that it can cause problems, since two different versions are trying to use the same files. I didn't run the two linked for very long, so I can't say for sure on that part, but I would highly recommend unlinking the two.
The only downside of unlinking the two is that you'll have an extra folder inside the "Nintendo 3DS" folder, but if you don't use the sysNand for anything other than launching the exploit, that folder will be very small and not use up much space. (On mine, it's 5.06 MB.)
Most guides I've seen suggest setting up emuNand and then doing a "Format System Memory" on the emuNand to make it "clean", or even formatting both nands. I actually performed the format on sysNand and never did it on emuNand, so my emuNand kept all the stuff I had previously (Mii Plaza progress, other save files, etc), and I haven't had any problems doing that. So if you've already been using sysNand for a while, I'd probably recommend formatting only the sysNand to unlink them.
Installing a system update doesn't remove any installed CIAs, but I would STRONGLY recommend using emuNANDTool to back up your emuNand partition before ANY system update, just in case you do run into an issue. Also, when support is available for the newer version, to be on the safe side, only update by going into System Settings > Other Settings > System Update (page 4). Make sure the version on the top screen matches what you expect to see (has GW, is the proper emuNand version, etc) so you aren't accidentally updating your sysNand and locking yourself out.
