There are a few parts to this question.
The first is: I'm running a virtual machine guest using vmrun and nogui, when I open the VMWare Fusion application, the window library opens but subsequently also opens any window of a running VM. Is there a way to prevent this?
Secondly, but related: Once it does pop up or I have that separate VM Window open, is there a way to close the window such that it does not suspend or shutdown the vm i.e. convert it back to nogui mode?