After a few hours of trial and error, the manufacturer specific structures have been created.
I will briefly describe what I did, in the hopes that someone knows an easier method.
The Types page from Profiles.xls was copied to a separate file, I happened to name it itypes.csv, and added my changes.
The Messages page from Profiles.xls was copied to a separate fie, that happened t name imessages.csv, and added my changes.
For good measure, I made Profile.xls match the new csv files.
I changed the config.csv per my needs. A word of caution, if some part of FitGen doesn't like the additions in config.csv, it will remove them from the file.
Lastly, the command used was: FitGen -types itypes.csv -messages imessages.csv -c. Doing the options separately results in config.csv getting overwritten.