The way I'm doing it is to write the tactical and strategic games as pen and paper/play by e-mail games. This serves as my design doc. Once I have all those systems in place, I can start planning what kind of user interface and AI I will need to automate the tactical and stragetic systems.
Some perks to this method is that I can play test the game before I even write a line of code. Also, a lot of the art resources used in the manuals are now my concept art or they were created from 3D models to begin with.
If you're interested in how I did it, my rules for Cluster War are available in my TCOM Gallery at:
http://www.geocities.com/tzircher/tcom_gallery.htm
Without trying to come off as a pimp (grin), here is some info on Tactical Command 2nd Edition, the combat system for CW:
http://zircher.iwarp.com/tcom2.htm
CW/TCOM2 is designed to be generic and easy to adapt to different sci-fi backgrounds. I don't know if it would work for your vision of a tactical combat and space empire game. But, they might prove to be solid basis on which to explore your own ideas.
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TAZ