I have done a great deal of that in the past (it's how I earn my living), formerly with film, and now with digital equipment. Check this APUG post: (there was a url link here which no longer exists)
Yes, you should polarize the lights, but I would reserve the use of a second polarizing filter over the lens (called double polarization) for special tasks. The light polarizing filters will solve most reflection problems, but when you add the filter over the lens, virtually all reflections will vanish, and you will see a dramatic increase in contrast and saturation, which is usually much too much for transparency film.
I usually reserve this technique for situations where I was photographing paper (such as a drawing or pencil sketch), or a very old photographic print, where the edges had "silvered out." When photographing paper, close examination of the transparency will show that some of the paper fibres show specular highlights; double polarizing will most often control that. Another idea is to rotate the original 90°; this works especially well if the paper has a "grain" to it.
With digital, contrast and saturation control is much more easily achieved; with conventional colour materials, you may have to push/pull transparency film to get the desired results. I have used Kodak duplicating film, in both the sheet and 35mm formats, when an original was highly saturated. One example which comes to mind was when I had to copy several Cibachrome prints; I copied them on Kodak E Dupe film, using electronic flash. As I recall, the filter pack was something like CC40C + CC80Y, with an effective Exposure Index of about EI 10, which meant f/22, with about 8 flash "pops" in a totally darkened studio.
Drop me a PM if you have any specific questions.