Maybe some general things about the Rebuilder
Source Folder - cmpro scans this folder (and optionally subfolders) for valid files (either single file or file in archives....or file in archive in archive..or ...). This is done by a hash lookup against the loaded database. In case of a match, each instance will be generated in the destination folder, now using the correct names. Each instance means that if a file is used in various sets, each set is being generated (if not yet existing) and the file is being added.
Destination Folder - here the matched files are being re-generated with correct names.
You need various source folders?
Then you can either setup folders as 'AddPaths' in settings->addpaths and enable the "use addpath" option below the source folder edit box.
Or you can drag'n drop files, folders directly into the rebuilder window (by the way, drag'n drop also works in the scanner...which then internally runs the rebuilder).
You need various destination folders?
Ok, a bit more tricky, currently you can only use system-default-folders for this, i.e. you can split up sets by bios file usage.
Recompression should usually be turned off....a later run with batch tools to rezip files is a better approach...or drop them in my zipmax tool

Things which make rebuilding slow:
- Recompress enabled (speed killer)
- remove rebuilt source files (useful feature..but of course this is additional effort)
- an enabled Rebuilder Advanced->additionally test md5/sha1 (however this avoids rare crc32 hash conflicts)
- Advanced->backup replaced files
If you know what you're doing you can fiddle around with these features to get some speed up...