Hi semper_fi, I take it you are using the old version of Sanctuary and not the one in this thread? Not sure what you mean by the MTS version- I haven't uploaded it to MTS.
The schools will usually be chosen according to the nearest- but that will sometimes be nearest as the crow flies (in a straight line) and not nearest by road/ route. I put more than one school in because with the original version I noticed that when my population got large there was a bottleneck, and sims were missing school. Adding extra schools solved that. If you wish to control the specific school that a sim attends then you will need a mod (such as Twallan's Career mod), otherwise the sims will just attend whichever one the game assigns.
For the Story Progression problem, I suspect that may be a problem with either the way SP is set up (do you have work push activated, for example?) or else perhaps another mod problem. I noticed someone on the NRAAS forum having the same issue (was that you?):
http://www.the-isz.com/nraas/index.php?/topic/2132-sims-no-longer-go-to-work/page__pid__38241#entry38241If you are using the old version of the world then there are no subways.
For the secret lots question, I meant the lots that are accessible only by dive well (Duck Island, the Geo Dome garden). You could mark those as 'No Visitors Allowed' which will stop sims trying to autonomously reach those lots (in the new version, they are set to that anyway).
I would urge you to download and try the latest version of this world if you haven't already, as I made a lot of improvements to make it work better.