I'm not sure you can run two instances of WFA on the same system, but if the reason you want to do this has to do with the need to export DAR files compatible with older versions of WFA, this might help. It is un-supported but I think if you aren't using higher-version features you can manipulate the DAR file (which are .zip files if renamed .zip) by replacing the MANIFEST file inside the .dar/.zip file.
I've attached a zip file which contains manifest files for WFA 2.1, 2,2, 2.2rc1 and 3.0rc1. If you rename the .dar file to .zip, expand it, replace the manifest file hiding inside, you can make a dar exported from 3.0 to be importable by a 2.2 system, etc