Could be confusing this one. It should be possible to do the set up from your Nvidea interface. I have not used Multimon so my help is limited.
But if you go from the Nvidea interface and select the primary to be whichever you want and select "extend my desktop" to the other screen it will or should perform as you want it.
EG. If I want a program to open and run on my screen 2 I open it on screen one in the usual way then drag the window (not maximised ) to the second screen where I then max it. My e-mail sits there for example and on boot up it opens in the screen 2 each time.