A couple suggestions for new works as people post them:
1) Over on The WWOMB, there was a whole classification of crossover stories where the fandoms were listed as one, aka "N.C.I.S./The Sentinel". But that isn't the format that we should be using here, since we have everything we need with the new software package. So if you have a crossover between two fandoms, just list those two fandoms, and don't use the old fandom names. So in the case above, you would list both "N.C.I.S." as well as "The Sentinel" for your two fandoms.
2) Again on The WWOMB, we had a naming convention for characters and relationships that included the fandom, like "Dr. Perry Cox [Scrubs]". All of those characters are imported, and believe me, the fandom names helped me migrate folks to the correct fandoms, which was a huge job. But going forward, if you want to add a character that's not in the system, say "Sean Kelly" from Scrubs, or a relationship like "Elliott Reid/Sean Kelly" from Scrubs, then just add it without the fandom name. Now that we're up and running, we don't need the fandom included as part of the name.
And again, if you are importing from AO3 to SqWA (or SqWA to AO3), use the information in this post as a guide.