I would not use the CD Wizard to move clips around in an existing montage. The Clips tab lets you control the start/end times (and other things) of the actual audio files, and the Markers tab lets you change and manage the marker timing placements among other things.
By default, the CD Wizard binds the CD Track Markers to the start/end of the appropriate clip, but you can always unbind the markers from clips and/or manage markers separately from the clips in the Markers tab settings.
When you say, “otherwise i can type in new values up in the CD window just fine”. Do you mean the CD Wizard or the CD Tab?
Either way, I think you would be best to manage the placement of your audio files/clips in the Clip tab if the montage is already started.
PRE-GAP in the CLIPS tab is the amount of space between a clip’s starting point, and the end of the previous clip. So in other words, it’s the space between two audio clips. The PRE-GAP of CD Tracks can be different, depending on your marker placements and marker types.
If you check the “Functions” menu of the clips tab, you can choose “Align Clips” to move multiple clips around in an existing montage, but if you need to just move one, I usually just use the Clips tab. If you keep Ripple settings to Global, changing a clips position will keep the relationship of the following clips the same.
So, you have to be clear if you’re trying to adjust the spacing between audio clips (audio files), or the spacing between your track end and start markers which results in a negative time count between songs. If you use CD Track Splice markers, then there is no actual pause time (as it’s traditionally called), because the spacing between songs is built into the track times and not between track markers like the old days.
Once you are done rearranging a montage, you can go back to the CD Wizard, and turn off all options in the CD Wizard except for the option “Quantize CD Markers to Nearest CD Frame”. I do this so often that I made a CD Wizard preset with just that setting active. I hope someday PG adds a special shortcut to “Quantize CD Markers to Nearest CD Frame” so it can be done without using the CD Wizard.
The CD Wizard is great when you first lay out a CD, and to re-quantize CD Track Markers if things move around, but for additional editing of clip timings and marker placements, I would use the Clips tab to change the timing of audio files in the montage, and then the Markers tab is to change marker placements if you are not happy with their placement by the CD Wizard.