"Right now, I have to create separate Easy CD Creator projects for each group of files within each folder"
Not sure I quite know what you mean.
This is not any easier way, but the way I handle projects that are over 700MB.
Burn the main important folders "edits", "images" and as many of the wav files out of the "audio" folder onto one CD. (using the shift key as Doc suggested to select multiple files, noting where you left off for burning the remaining files to the next disk)
Burn the remaining wav files onto another disk.
Maybe that's what your doing, sounded more complicated to me, maybe not though.
I don't think there is an easier way. And if there were I probably wouldn't trust it anyway.
When you look at as organized:
-The image files in the image folder, graphics of the wav files, edits in edit folder.
-The *.npr file which is your latest mix settings/revision (and where the wav's are located in the project along the timeline, very critical)
-The wav files themselves.
So, as long as you keep the folder structure intact, your fine. (for rebuilding the project, do the restore in reverse)
Sorry if I'm stating the obvious.