It sounds like you have already set everything up - if so, then all you have to do is to save the scenario, and when you start if off, just select the factions you wish to have played by real people. You can assign the passwords during the initial turn (which you would play as CMN).
If this isn't what you are wondering about, then perhaps the information you want can be found in
this article by Googlie, which covers nearly all of the scenario-building process.
Regarding the Uni techs, there seems to be a degree of inconsistency as to how that will work; I often find it necessary to mess around with alternative approaches to get it to work as expected. In one game I had 2 Uni factions and they behaved differently regarding the initial tech assignments, one of them querying for the extra tech on turn 1 and the other not, so go figure.
