I am ashamed to even ask this question and will be more ashamed when someone points out the obvious answer (or where I should have found it).
I have hunted high and low and cannot seem to find any reference as to how to set the memory settings for the Config Tool (C:\AwareIM\bin\ClientStarter.bat) when running AwareIM as a service.
this can be controlled in the ClientStarter.bat file itself. Take a look at how this is done in the startAwareIM.bat file and do the same in the ClientStarter.bat. Off the top of my head: