Here's a Youtube video on adjusting the Bowden tube. As you can see, most of us have the sag on the downward side of the tube and the amount of sag is determined by how many spacers are used on the tranny end of the Bowden tube. Just rotate yours around so it sags downward when you re-assemble everything.
The video guy has fancy spacers, but plain old flat washers from an ACE hardware store that fit the OD of the bowden tube metal collar at the tranny end is fine. You don't have to remove the cable to add spacers, but if it's loose anyway it's pretty easy. If the cable is already assembled to the tranny, cut a notch the width of the clutch cable into the spacers to form a horse shoe to fit over the cable, then put some vice grips on the throw-out arm and lever it forward enough to expose the cable by pulling the Bowden tube out of the bracket (tranny end). Slip the spacers over the cable and onto the Bowden end until you're stack-up gives you the proper sag. Release the vice grips and you're done.
The proper amount of Sag is 1" - 1-3/4" (use a straightedge along the length of the tube to measure the sag).
BTW: As mentioned already, the cable should exit the tube on the tranny end from the middle (more or less) of the exit tube. If it's dragging a lot at the top or bottom lip and cutting into the Bowden end nipple then it will prematurely wear and fail. If the cable is just touching the nipple and not wearing into it, I wouldn't worry about it.
Don't forget to fill the Bowden Tube with grease while you have it out of the car. any decent automotive grease with molybdenum is good.
Here's some more good Bowden tube info from Rob and Dave:
http://www.vw-resource.com/bowden_tube.html