I have a substantial number of folders that I want to move to a new user so that the list of my active folders is more manageable. Right now all of the folders I want to move are in a single tray. Is there a way I can identify all of messages that belong to those folders so that I can move them en masse to a new user folder? And if so, how to keep the messages in the same folders.

There are two ways.

1. Add the other users mailbox to your folder list. Create folder structure you want in the other users mailbox, then copy messages from your folders to those deleting your folders once you have confirmed a successful copy. Unfortunately, you must work at the message level. You can't copy or move entire folders from one user to another this way. FWIW, I prefer this approach because you see what you are doing. BTW, when copying messages you can open a folder, do a Crtl+A to select them all, and then copy them all to the destination folder.
2. Identify each folder's filename and then, with Pegasus Mail closed, copy those file pairs (.PMM & .PMI files) from your mailbox directory to that of the new user. You will then need to create the appropriate tray structure in the folder list of the new user. Once all is well is well for the new user you can open Pegasus Mail as you and delete the folders that are now in the new users mailbox.

If your goal is basically to archive some folders then their might be a better solution. It would allow you to attach/detach these folders to your folder list at will. The process is similar to #2 above but would not require a second user.
Post back if this sounds appealing.