I used to do this for a living when I ran my own company and it really isn't that hard to do the physical work, but your zones need to be designed correctly. I really never designed the zones, as the vendor did it for free if we purchased parts from him.
They sell automated valves for doing this kind of thing in Home Depot etc, but if you are doing to go through the trouble of renting a ditch witch, and trenching out your lawn, you might as well go the full distance and install a proper irrigation system.
It isn't rocket science, and there is a CP member who has a thread in the Power Ring forum that looks like he could help. I will see if I can find the link.
http://forum.calgarypuck.com/showthread.php?t=114968
Like you are mentioning, you would likely need to leave your house at 2 boxes and have 2 sets of valves. The valves and your control equipment are likely the largest cost in all this, and if money is a factor, you could likely lay the irrigation line, put in proper heads and then use something like this:
to just run from your lines on each side and allow for you to manually turn each zone off an on. You will likely need 4-6 zones on a normal residential lot.
Then you could just do the other work at a later date if you decided to.