Having multiple profiles on one computer is fine, but you only install Mach4 once. Use Mach4Loader to select the desired profile, or edit your desktop launcher to start the desired profile.
Having two SmartBOBs plugged into your computer at the same time will not work because the first one found is the one that will run, regardless of profile. You will need to plug in only the one that you intend to run at the time.