As Bleiente says, use MultiSH4 to make yourself Save folders of different names for the two separate installs. You don't want RFB Save files getting mixed with OM Save files in the Documents / SH4 folder. Rename the folders, such as RFB and OM7, or whatever you want to reflect what they're for.
As for the Uboat start in Steam, had you "imported" OM to the Steam Library? That might be your OM start short-cut. The way SH4 is set-up, the German side and the American side share quite a few files, so your start screen (and a few other things) would be for whichever mod was activate into SH4 last. The German side will also reach across and use some of the American campaign files. They are usually compatible, but not always, RFB with RSRDC on top of it should be nearly 100% compatible with OM. You will still run into the fact that the two sides share interface elements though...
