All very good answers here. However, I do this all the time and I have noticed that the two AVIs are not always using the same metrics. Let me explain. One may be a different in resolution than the other video or even CODEC and audio parameters may be unequal.
This is what I do:
(1) When I download my CD1 and CD2 in uTorrent, I boost the priority of the CD1 to HIGH, while CD2 is being downloaded at NORMAL. This makes CD1 ready before CD2 is finished.
(2) I start converting CD1 to a DVD, while CD2 is still downloading. They are happening in parallel.
(3) When CD2 is downloaded, I convert CD2 to a DVD.
(4) I glue the two pieces together using DVD2ONE, and I use the option called SEEMLESS JOIN (Its the buttonwith a double plus sign). I end up with a chapter mark at the CD2 demarcation with perfect join.
(5) The gued toether movie is also compressed, if needed, because DVD2ONE is also a shrinker and everything is perfect as the final DVD.