To your first issue:

The rebuilder adds/creates files to the chose destination ONLY. If you setup one destination rebuilder path, new files will be added there and not in 2 different paths. You can use multiple paths by using the system-default paths. Depending on the set system-default paths it choses the right one.
I think you may talk about fixmissing which is totally different from the rebuilder. Fix missing searches the addpaths for missing files and has some rules to add them back to the collection. If the set with a missing rom is partly available in a rompath, fixmissing adds it to that set. If the set is completely missing, clrmame uses the first rompath (see settings) to add them. An exception is twhen you selected the advanced option "use sys-defpaths for fix missing". If that option is enabled, fixmissing will use the assigned path if a file is missing.


your second issue:
Yes, your backup folder can contain files which are needed. The unneeded check checks the current set (parent or clone) for possible unneeded files. If the file is not listed in the datfile it is unneeded. The fix option (with backup enabled) puts it in the backupfolder. So far...so good. If the file has to be moved to the parent or the cloneset, fix unneeded will handle that for you as well. If the file is needed by a set which is not in a parent/clone relationship it is put to the backupfolder only (since the other set to where it belongs isn't scanned yet). So theoretically you got valid, needed roms in the backup folder.
Fixmissing automatically looks in the backupfolder, too. You don't need to setup the backupfolder as an additional addpath. The problem: normal fixmissing looks in the backupfolder but it only looks in the current setname archive/folder there and possible clones. You can enable the advanced option "fix missing scans all sets" if clrmamepro should scan all files in the backupfolder....but this can be a MAJOR slowdown since it scans all files for each missing file. A rebuilder run with backupfolder as source afterwards is the better solution.




Hope this helps a bit ;)

Roman Scherzer
ClrMamePro