You may need to synch the two sources song-by-song but again that's just time and not hard to do at all, for example, in Adobe Audition. If you're lucky, you may only need to do it once for one of the complete recordings...
With two digital sources you should never have to split either. Use something like Sony Vegas where you can visually stretch/shrink one to match the other. I THINK Wavelab can do it this way also. Using analog sources that can vary in timing should be the only occasion you'd have to split into segments.
Good comment. I personally agree as I've never had to split them up, but people that I know have said that they had to do it song-by-song...not sure why though.
BTW, as mentioned previously Audition does this very nicely.
What I do is use the stretch/shrink function. First I make sure there are no dropouts in either recording by comparing the timing of both recordings side-by-side. They should be relatively parallel without any step changes in timing between the two. Obviously, if there's a step timing change, then you probably have a drop out.
After confirming that there are no drop-outs (or if there are, fixing the timing of one of the sources to match the other) I check the exact timing of a specific event near the beginning of the sources...say a drum hit. It needs to be a single point source of sound so that you can get a precise timing measurement. Note the time of this event on both recordings.
Then go to the end of the show and do the same thing.
Figure out EXACTLY the amount of elapsed time that occurrs between the two points on both recordings. If there's a slight difference (which there probably is) then you have to stretch or shrink one of the sources so that the overall timing between those two points is exactly the same on both recordings. Obviously, you want to use a ratio that makes both the exact same length...if you find this function in Audition, you'll be able to figure out how to do it. It's not hard to figure out.
Then after stretching/shrinking one of the sources, go to the beginning of each recording and select another EXACT point where both sources will start. Trim one or both tracks so that they both start at precisely the same nano-second. Obviously, since both tracks are now the exact same length between the beginning and end, they should match precisely after this step.
OK, now load both tracks into the multi-track view of Audition so that they lay parallel to each other and play both at the same time, making sure that both are playing at about the same volume percentage. You can mute one at a time, mute them both, or play them both simultaneously in this view. However, in this case you want to play them simultaneously and confirm that both tracks are aligned properly by listening at 10 minute intervals throughout the show. If the tracks diverge from each other, it will be obvious because the show will start sounding more and more reverb-y...the more the tracks diverge (the later in the recording) the more reverb you'll hear.
Obviously, if you hear any reverb, then there's some more work to do to adjust the length of one or the other sources...the goal is to have the match exactly so that there is no reverb at all.
If you don't hear any reverb, it's time to decide what percentage of each track you want to be able to hear in the final mix. I just goof around with the them and listen to the mix until I find a combination that I feel sounds best.
Viola!