In protools you can align the audio pulses in one track, like the kick, with the pulses in another track, like bass notes, using nudging. I am not sure what the left and right movement keys are but basically you can push an audio clip left or right slightly, test the sound and then go to the next clip.
You can also take the timing from one track and insert a series of audio clips on another track which exactly match the original. Say you want a lo end synth pulse to match a kick drum. First you extract timing from the kick drum audio track then you paste the pulse track automatically at every kick pulse but of course in its own track.
You can do this in Sonar but its very labor intensive.