I would, yes. Database and files should still be present as like avatars for members pictures...I would put the XF files on a subdomain and you can change it after all the import data is transferred over...the importer uses uploads as a directory that's required.
Another newbie questions. I install XF in a sub-directory - is it trivial to move this to the main web root once I have finished the import or do I have to just change Apache virtual host entries to point to the "new" webroot.
Once everything is imported, you will go into your setup options...you will go to basic options after you move the files over to the root directory.
You can think replace the sub directory to the main root directory.
I liked MyBB but its basically almost tumbleweed on their community boards. I can understand it is free but it does not seem actively supported at all. I am pretty much convinced to change to XF.