You'll have to launch the standalone v.1 of MMV, then export your patches/banks. Hopefully you've kept them fairly well organized. After you export your stuff from version 1 you can then launch version 2 and import the file(s). A pain, yes.
I always save my patches in a bank with my name, then a subfolder for each song, then a patch name with the name of the song, that way I only had to export that one bank and bring it into version 2. Pretty painless for me. Good Luck.