Keeping the subhoods separate worked best for me. Sadly my Megahood was one of the original ones and totally corrupted. I also lost it in my computer crash. I might start a totally clean one up, some time.
I like to have each one with slightly different rules - different season set ups for example, Strangetown was always sunny, Veronaville mainly rainy, and I have a list of job restrictions, so that it makes a bit more sense. Riverblossom Hills is supposed to be remote - you can't get a job in a big business or law firm there, you need to move to the city or suburbs. Military sims need to live in Strangetown (I arranged some very uniform, military-like housing in a line there) or travel to the base and leave their families for days at a time. Some of the hobby-specific careers were supposed to be based in Desiderata. And there are slightly different cultures, so people are kind of afraid/racist towards alien sims in most places except Strangetown, for example (and in Downtown they don't really care). Somewhere like Riverblossom, everyone knows everyone's business, and you go to church on Sunday, if you don't, people think there is something suspicious about you. Also Plantsims are normal, whereas anywhere else they would be surprising. Veronaville is a bit theatrical/fanciful/magical, and people don't think it's weird if you wander around in costume or face paint. It also seemed more LGBT friendly to me than some of the more stuffy/traditional hoods (although perhaps that's Andrew's influence!) so my sims who were afraid of being judged elsewhere tended to gravitate towards it. Veronaville natives are generally so wrapped up in their old feuds that they don't give much of a hoot what everyone else is doing!
Sims can walk to lots in their home subhood, but must use the taxi or a car if they want to travel to a different subhood. I should use that mod that charges for the taxi, too. I use "localwalkbys" to make sure they only encounter walkbys from their own subhood, and make extensive use of the visitor controller to control who shows up on community lots as well - some are local only, some make sense to travel to, but most (except the hyper-local ones) are also restricted by things like hobby and aspiration, so you'll meet like-minded sims on community lots, which makes them worth travelling to. Services may also be different in different hoods - if it doesn't make sense for there to be a pizza delivery restaurant or maid service locally, then you can't call for these services. Of course the emergency services are available everywhere.
I set up playable schools and keep a list of pupils for each one, this is based on where they live. I used the school bus hack so if kids asked to bring a friend home they weren't supposed to have met, I could cancel it, and allow it if they were actually supposed to be at the same school.
Pleasantview Primary school - a fairly standard, modern, suburban primary school with good varied facilities. Also takes kids from Veronaville and Desiderata Valley.
Riverblossom - the kids were "homeschooled" by the old ladies that live together. Traditional and old fashioned. They did gradework every morning and then in the afternoon, the kids were split into girls/boys with the boys learning mechanical, farm work and fishing and the girls learning cooking, cleaning and sewing.
Strangetown - there were too few kids and it was meant to be remote so I homeschooled everyone, but I did toy with having a boarding "military school" on the Grunt lot. The problem was nobody in any other hood was wayward enough to be sent there! Maybe Dustin Broke or Lilith or Rick Contrary... maybe if I play it again. It could be an automatic referral for any D grade or police visit
they would have some fun there, and maybe some would enjoy the structure. The main problem is that I can't see the Grunts accepting the Curious bab(ies), nor the Curious brothers wanting their kids to go there, I was thinking of setting up a scientific institute instead that they would run, but never got that far.
Private school - some unnamed central location for the rich kids to go to. Never built it. I think I split up girls and boys, but I can't remember. The private single sex schools I know in real life did have some kind of arrangement so that the pupils could meet each other regularly and make friends, but they never had lessons together.
Belladonna Cove - a run down primary with very little space and therefore limited facilities. Also takes kids from Downtown and Bluewater.
Downtown High School - for all the teens except Strangetown and Riverblossom.
I did move a few sims between hoods. Not a lot, and I can't remember all the sims I moved but anything that made sense to me job or story wise. The scientist with the two children from Belladonna moved to Pleasantview and I made them friends with the Goths. His wife became a self-employed marriage counsellor and tried to save the Pleasants. Alexandra Pirate or whatever her name is moved to Veronaville, where nobody thought it was weird that she was a pirate. The Summerdreams became witches. The twins from Belladonna Cove also moved to Veronaville, where more of the magic is.
The three universities were tiered and I restricted the subjects available at each of them. Minimum grade requirements were different for each. I had the unicareershack by SyberSpunk and changed which majors boosted/unlocked specific careers.
La Fiesta Tech was a technical university, specialising in science and maths - Maths, Physics, Biology. Min grade required B - it should be accessible, but the subjects are hard and that's reflected. Some careers you need a specific one of these to get into, otherwise they just give a boost to more careers.
Academie Le Tour was the more "academic" or elite type one - Literature, History, Political Science. Min grade A, as it's meant to be elitist. Again these unlock some specific careers.
Forgot the other one's name - but it has everything else - Art, Drama, Philosophy, Psychology, Economics - minimum grade C. These majors boost certain careers but nothing is solely unlocked by them.
I moved a LOT of the uni students either to match their major or just what fitted to me, I also gave some of them different majors to fit the uni they were already at.
I use the sims as a psychology simulator...