I have a similar application. I have 3 versions, current, n1, n2.
What I do is use the Xenapp BrowserName filter/condition to apply the variable. So if browsername is current, then set the variable current to 318 (which is the app path). I launch the vuecmdagent.exe as the executable with the parameter being c:\path/%current%/name.exe and likewise, c:\path\%n1%\name.exe
If there is a version change, I only need to set that in WEM to make 319 current, 318 n1, 317 n2 then.