hmm, i used to have similar problems with the program i used. then i forgot what i did, but i havnt had the problem since. haha
welll, if you record the different tracks at the very beginning, just press the skip to beginning button or whatnot. that should line it up. you can also move the second track a bit to line up with the first.
i bet these other recording giants can help you much better than i. :p