I'm currently using this nVidia nView driver option.. but I would like to know how do I set up certain things to be executed on start-up on the X desktop and others on the other..
Does anyone know anything about this ?

I'm looking at it now and as far as I can see, all the desktops still have the same processes running, which makes sense. So, if you was to execute a program, it would execute it from all the desktops.

So the answer to your question is that it is not possible.

if the program remembers its screeen position, then it will open on whatever screen you left it on. If not, i'm not sure, but Ultramon may have options for this.

It's possible adding special setting for each application. On the menu at the right side you shall see APLICATIONS, right there you can add special settings for each program, like opening it on any screen you want, follow these steps: