Well you probably won't know for sure until you start setting up MultiSH3, so good luck! Usually with multiple installations people install one time and then just copy the game folder to multiple locations, so let us know how it works out.
IIRC you can download MultiSH3.exe from Subsim if you don't have it already.
It is very simple, just an .exe file that you copy into each game installation folder and run once, it will let you specify a unique 3-letter name for the My Documents folder that each installation creates. That way career files and savegames from multiple instances of the game don't get mixed in with each other.
I would think that if it won't work the Steam game installation itself, you can just let that one use the default "SH3" folder name and then put MultiSH3 in the other installation and use it to specify a different folder for that one.
