Hi,
so quick answers only since I'm nearly off for a while due to holidays...but here we go:
1) as long as you already got sets in already have folders (setup as rompaths), the systems -> auto assign button will assign them fine. If not, well, you need to find a way to generate the folders, add them as rompaths (simply drag'n drop in settings) and assign them as system.
General question is if you really need to use system default paths at all. If you want to split up your sets by bios, yes, ok fine..then you can set them up. If you use the MAME + software list mode, then too..however it's a pain the ass to use this mode....you should prefer single profiles per software lists.
2) You need to double-click the last column in systems dialog to edit/add the path (or as mentioned before use the auto assign button to map rompaths)
3) The rebuilder is an "adder". It takes anything from the given source, matches the checksums against the database and recreates each matching instance in the destination. So you can use it to add new sets to a collection...or change one emulators collection to another emulator's one...etc...So...you decide where to rebuild the files to. But you need to understand what the rebuilder is....a file based check and create/add mechanism...not a "my destination will have complete sets" magic tool.
4) Such a message appears if the database got some problems regarding identically named roms while the binary content differs within a parent clone relation. If you would simply merge them, one file would overwrite the other (due to the same name). But they do differ. So that's why cmpro renames one of the files, so you don't loose any.
5) "Never show up" ...well..what do you think you do with drag'n drop? The scanner can be setup that drag'n drop runs a rebuild operation. And as mentioned, the rebuilder takes the input , matches the data against the database and when it find matches it creates the files in the given destination where it uses the right names. If nothing is created, nothing is matched.
6) prestring...so again rebuilder. Yes, the rebuilder copies files (when matching is found). Only if you enable the remove rebuilt source option, they will be moved. And of course identical roms maybe used in different systems. So if BIOS A / Set AA uses a rom with checksum 0x12345678 adn BIOS B / Set BB uses the same one, both instances will be created...one in B and one in A.
and now.....holiday