Back when I was playing SH3, I "copied" my vanilla Silent Hunter 3 1.4b by right clicking on the SH3 game folder where it is installed. Then clicking Copy. You will then have 1 copy. Do it again and you will have Copy 2, and so on.
Back then we didn't have Multi SH3 and a way to have different copies we could play with it. So I don't know how you'd get these copies to run with Multi SH3. But someone should.