Many of the things that need to be done to beef up the starting situation, if that is what you are talking about, can be done in a sort of hodge-podge order via the scenario editors. As I recall Googlie's article, it covers the initial setup very well
; it gets the factions set up and initializes all their preferences, techs, etc, and putting down units. but does not give much guidance when it comes to creating and enhancing bases, or much about how to set alien (Native Life) lurkers or try to get the computer controlled factions to do what you might want. Goog's guide gets you off to a great start, however, so it is a good idea to use it as a script or checklist.
Bases can be placed by first placing Colony Pods on the sites, switching to the appropiate faction with the Scenario editor, toggling the ScenEditor (so you are in play mode), and then starting the Bases (with the "B" command as you would in the game), then toggle the scenario editor back to its editing mode (one of those modes is considered 'activated', but I don't remember which mode that is). Cycle through each faction as necessary to get whatever bases started that youi wish.
Once the bases exist, the ScenEditor can add facilities (prerequsite techs can be temporarily added, just as for units) and population in its edit mode (various additional buttons and options appear on certain standard screens when in the ScenEd and can be easily overlooked as the rest of the screen looks so familiar). This can save you a lot of time compared to playing the factions, allthough once you've got everything set up, you can reset the year to whatever you want, so even if you play a few turns, you can turn back the clock.
The downside is that the ScenEd is a bit quirky, the more so when you are still early in the learning curve, and sometimes it does nasty things, like abruptly exiting and ditching all your currently unsaved stuff
. It is also possible to get scenarios into such an effed up condition that they seemingly cannot be repaired, whether by its fault or the users, so I highly recommend making a sequence of backups (lest you replace your last good version with an effed up one before you learn that is is bad) and to make these backups at fairly frequent intervals. I usually also save the map separately whenever I make changes to it I would not want to have to redo. It is not a bad idea to try out the scenario occasionally just to make sure it doesn't have some horrible
defect that could set you back many generations of backups to recover from.
Once you get the hang of it though, it can be quite powerful and while not exactly unmitigated pleasure, still 'not bad'. If the ScenEd gives you too much trouble, perhaps you will feel better if you just put a couple of interesting 'surprises' next to the likely base sites or lurking in the middle of a group of resource bonuses
.
Good luck and have some of that 'not bad'.
