Well, the move from 1.9 to 2.x can be really quite disrupting. Things changed a lot regarding the file system. And the "ftp and choose/link" workflow doesn't work anymore. You really need to spend some time working with it all to understand it. Once you "get it" it is not so bad, but it seems to be hard to explain.
Basically you can FTP a file into a repository. Hooray. But to get that file to appear in your course you will have to actually use the file chooser to go and select the file. Then Moodle will do a little magic to create a link to it that works on your page/label/question.
That means that you can't do something like FTP up 1000 audio files, and create question import file that links to each of them, and import it. You need to use the file picker. One file at a time in this case. That has been painful for a lot of us.
The workaround is to just FTP all your files into a web accessible directory on your server and then link to files in that directory. This works and I do this for the above situation (1000s of audio files, one per question). But beware, backup and restore and the file chooser won't know anything about your files.