[Wine] Multiple apps within a virtual desktop

[SoAnIs]

TL;DR version: I have 2 apps running in a virtual desktop, I need one of them to be in always-on-top mode. How do I set this up?

Full explanation:
I have EVE online running in a virtual desktop, EVE:
wine explorer /desktop=EVE2,1600x1200 /home/USER/.wine/drive_c/Program\ Files/CCP/EVE/eve.exe
I also want to run ScanAid (http://eve.grismar.net/wikka.php?wakka=ScanAid) (a little scan helper program for EVE) in the same virtual desktop. This works:
wine explorer /desktop=EVE2 /home/USER/.wine/drive_c/Program\ Files/ScanAid/ScanAid.exe
I need to have ScanAid always on top, or be able to switch to it (on-top is better). As it is I can get ScanAid up and running, and even displaying the helper circles, but as soon as I click on EVE the EVE window comes to the top and I can't reselect scanaid. Alt-tab just tabs between my actual Linux windows.
It seems to stay on top outside of a virtual desktop, but I'm running 2 eve clients, and thus need to be able to switch between them.