Hi Keith,
On the Tascam, the only way to fade in/out is by using the faders. What I do is create a master on the Tascam, then copy the WAV file off to my laptop, bring it into Sound Forge Pro, and before I run it through Ozone to actually make the master, I trim off all the "pre-song" noises...throat clearing at the mike, humming tube amps, and so on. If I'm going to do a fade, I do it here, as the fade is perfectly linear, and I can make it as long or as short as I want.
An alternative at a much lower price point than Sound Forge Pro is Audacity, which I believe is still free, and should allow you to bring in the master WAV and take care of the trims, fades, and so on to clean up the intro and outro of the song you're working on.
As far as the tracks lining up, they all start at 0:00, so you can export a single track, apply effects, etc. in a DAW, then copy it back into the song with no change in alignment...I tried that once as a test, where I copied a vocal track out, then tested iZotope's Nectar on the vocal, and copied it back into the song. The hardest part is actually finding which track is which, because the track naming convention Tascam uses doesn't make it clear which is track 1, 2, and so on.
I've never had an issue with the tracks not lining up, although I will mention that you may hear some bizarre things in a song that weren't there before - when this happens, the fix is to copy all content on the SD card to a computer via USB, then format the SD card in the DP-24, and finally copy the content back from the computer to the SD card. The cards do need an occasional format to avoid errors, and has fixed oddball issues for me every time without fail.
Hope this helps!