Try to find a service manual that details adjusting the window and channels. Here's the gist though:

1. Remove door panel.
2. Roll window all the way up.
3. loosen the 2 bolts holding the window to the regulator, then loosen the three bolts holding the regulator to the door.
4. Push the window up and back (for front window) or up and forward (for back window).
5. Tighten the 5 bolts you just loosened.
6. Roll the window all the way down.
7. Loosen the two main bolts holding the front channel (or rear channel for the back window), and press the channel flush against the glass.
8. Tighten channel bolts.
9. Roll window all the way up and check for gaps. Make sure the window is flush. You can even spray it with a hose to see if any water gets in.
10. While you've got the door panel off, I would clean and lube the channels with silicon spray.

Your windows should be nice and smooth now.