I've got a 2006 Saturn Ion 2 sedan with a broken rear door window (not the fixed quarter-window). I've gone through the steps to remove the inner door panel and outer trim along the bottom of the window. How can the glass get inserted into the run channels?
Like the S-series, the quarter window should come out first. For both the Ion and S-series, the quarter window is bolted to the door. The 10mm bolt is behind the moisture barrier, below the quarter window. Cut the adhesive attaching the barrier, leaving some on both the metal door and plastic barrier (the adhesive will reattach more easily to itself than to the metal).
Unlike the S-series, the weather stripping is a single piece that runs along all but the bottom of both windows, and it must be removed from the door. The weather strip is glued along the back side of the door; cut the adhesive. At this point, the weather strip can be removed from the back and top of the door; it can be left attached to the front side. Lift the quarter window out of the door well and over the top of the door, leaving it hanging on the inside of the door.
The door glass can now be inserted into the front channel and lowered into the door well. With the window regulator level with the bolt access holes in the door, the bolts can be (loosely) attached, connecting regulator and glass. There should be a little lateral play in the attachment points; not tightening the bolts allows for the window to be properly positioned when the quarter window is reinserted. Lower the window.
Reinsert the quarter window, reversing the steps to remove it. Tighten the bolts attaching the window to the regulator.
The window glass is now in place.