This is something I do atm, once you know where you want the colonies to be fire up ISBoxer and build the colonies via multiboxing. This will ensure that all the structures are in the 'same' place. The largest issue I had when starting this was that the extractors were all in slightly different places so I had to do each planet one at a time. i.e. scan each planet in turn and place the command center first. Once that is done you use ISBoxer to build the colony.

As far as running the planets go I use ISBoxer to restart the extraction cycle and ignore the head placement, then one day a week I will do each planet solo and re align the heads.