1) Remove the current paths from the folders tab, add the new paths, select save.
2) Media Companion does not yet access directly the XBMC database, mainly because of the difficulty of relative paths (The path to a file from XBMC will be very different that that of MC)
3) Not sure what you are asking here, but it sounds like offline content. Offline movies are supported, just create a folder you wish to use as a holder for offline content, and add this folder to the offline folders list in Movie folders.
For each movie you wish to add, create a new folder within the offline folders directory, naming the folder using the movie title, eg.
offline movies\Batman Begins\
offline Movies\Star Trek (2009)\
When you next search for movies, these offline folders will be added to your collection.
This is not supported by TV shows (yet)