I was wondering if it is possible to bin by basepair in Gelquest?  I have T-RFLP data, and I think the error on the capillary sequencer is about 2 bp.  Because of this, I was thinking I might bin into groups of 3 bp.  Do you know how I would do that in Gelquest?
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Yes, you can. (Hyper)binning does not happen while analyzing the data but afterwards.

After detection and sizing of the peaks, they are automatically grouped in (hyper)bins according to their size (usually base size). The hyperbin width is chosen automatically by the software (for fragments up to 1000 bp it is set to 1-bp-resolution). If you analyse pulse field gel electrophoresis experiments with fragment sizes from 100000 to up to 1000000 or more, it would be useless to bin these fragments with a 1-bp-resolution.

To change the width of the bins, please use the menu item "Configuration" --> "Hyperbin Detection" in the main window. In the configuration window change the "Local maximum detection parameters - Hyperbin width" parameter to 2 or 3.