What you do is cut two of the tracks from one source shorter or you make one source longer.
Any two recorders will have slightly different clock rates, so if you can figure out the speed difference, then you can align them more precicely. For instance, I use the CHANGE SPEED plugin effect in Audacity to shrink my DAT masters down by .012% to match speed with my Zoom H2 masters. That seems to get me within a couple thousand samples per hour, which is damn close. Actually, I keep meaning to make a test program so that I can find out the exact ratio of the clocks. Maybe I'll do that tonight. . .
1- create a track which is EXACTLY 1:00:00:00 long (1 hour) and load that into my H2 via USB.
2- Hook up my DAT recorder's analog input to the output of the H2
3- record the H2's output onto the DAT
4- digitally transfer the DAT to the computer
5- line up the start of the DAT version with the master version and find out how many samples different they are by the end.
6- calculate the exact percent I need to time-compress the DAT versions to match the H2 as exactly as possible.
7- use that information to create more accurately time-aligned sources for "matrix" mixing of (usually) SBD and AUD sources from my two particular decks.
DO keep in mind that the speed of sound varies with temperature and air pressure, so unless those are constant (not in real life!) you may have to make some other adjustments to get the best possible alignment of your sources.