I would assume your problem is getting that third side to use the units..
if the prequsits and sides are set propelry they should build the right buildings.
as for the AI to use the units you will have to make the triggers side specific for each of the Space Marines and Imperial guard.
You will need to set the trigger as an allied general side, then give it the proper side that the trigger will work for.
I dont have any of my old RA2\Yuri AI stuff anymore or i would show a few examples.
and if its the buildings giving you problems.. I'll have to look into that further.
Hope that helps some..
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