IIRC, better track editing is one of those things that is always on the wish list, but never at the top. Partly because you can already do all of this, if sometimes in obscure or painful ways.
If the tracks from the .mps file overlap, the way to start is to run the Network Analysis tool on them. After fiddling with the parameters for a bit, you should be able to simplify all the overlapped sections (be aware, though, that this can seriously mess with altitude information if your GPS jumps around).
Once the duplicates are gone, you can start chunking up the network with the cut tool. Simply cut the track at each junction, until you have a set of segments which intersect only at their endpoints.
Now for the magic step: use the profile tool. Eh? The profile tool? Yep. Turns out that the profile tool is also the track merge tool. Shift-select all the chunks needed for a single trail (using the right-click menu as needed to reverse segments). When the trail is complete, right click again and save it out as a new GPX file. Revert the display to just the chunked up trail, and repeat the process for the next track.
It would definitely be nice if this were easier, but it can be done with the program as it stands.
Hope this helps.
-- Mark