Yeah, sorry I have been a bit behind on this - between my regular work and getting ready to move into a new house in a couple of weeks, I haven't had much time to spend on modding support recently. :-(
We have a build of the TFE in testing now that is somewhat better in this respect - it automatically sets its working directory based on the path of the table you are opening, and it looks for dependent tables in that path. If it doesn't find them, it prompts you with the name of the file(s) to move, and lets you continue with the loading process after copying them over. We haven't pushed it out yet because there are still a couple of bugs to work out, the primary issue right now being that if you cancel out of the prompt to copy the dependent tables over, it leaves the editor in a pretty messed-up state instead of just closing out. I should have time to fix that by the end of this week, but if you're willing to put up with that known bug and be a beta tester for possible others, we may be able to push out the current build into a beta branch somewhere for you guys.