With Win2003 Server...
You run only one instance of WAA1SRV.EXE.
In IIS, you create a "Web Service Extension" for WAA1GATE.ISA and set it to "Allowed".
You service multiple websites on this computer simultaneously this way.  First, create a single physical directory "cgi-bin".  This is where you put WAA1GATE.ISA.
 
Then, with each website, create a Virtual Directory "cgi-bin" and map all of them to the one physical directory. Now, any website url to "\cgi-bin\waa1gate.isa..." goes to the one right place.  I create an individual DLL for each website, the file name of the DLL being what you use for "WAA_PACKAGE=".  I have had six different websites running simultaneously.