Basic Multi-City Strategy

Of course, every player is different. Every build will be unique. This is what works for me and how I wish I had done it the first time. 

First city has the fewest city spaces, so it will not be the best for training. Plus you have to have an embassy to join an alliance, so it is probably there, along with your highest level hero. For these reasons, I think City #1 should be where troops live. Train them in your other cities and let them live in City #1. 

This will be your "Starve" city. Troops don't go away when you don't feed them, so let them starve. They don't mind. Resist the temptation to build a lot of farms. Use your troops early to hit level 6 goblin camps for Second City Relics. You can build your might afterward. Attack your neighbors for rss

Focus on homes and barracks in City #1. I would do 10 homes and 13 barracks, then 1 of each other building. If you're online more often, make fewer homes and more barracks.

Do not use your HBCs in your first or second cities. They are hard to get, so save them for your Third City. You'll see why. Save a Hero buff or two, like "Trains with Gandalf." That will help building times in your next cities when you assign a higher hero to Construction.

City #2 will be your first training city, but it the same number of city plots as your City #1. So, I would train more T1 troops in City #1 while you start building out City #2 and immediately start hunting Third City Relics. 

Start City #2 with a vault to protect enough rss to build your city. Build one of each rss field to Level 5, then switch back to city view. DO NOT build an Embassy, unless you rely heavily on reinforcements for troop kills. Don't build a 2nd Academy yet either, unless you saved some lower topics to research, like Saddlebags, Vigor, Hones Blades and Far Seeing. Watch Tower is optional too. Build 5-6 homes and as many barracks as you can fit. I would make City #2 a training city for T3 troops. Save your HBCs for your 3rd city!

Your available playing time will determine how you fill out your rss fields. If you're online a lot, don't build them out much; focus on farming neighbors for rss. Fewer rss fields mean more Idle Population to train as troops. If you're not online much, make City #1 your "Rss City" (an even split producing ore, stone and wood) and City #2 your "Food City" (at least 50-75% farms). I also don't like wilds, because it's annoying when they are flipped and I don't have many rss fields built out. That's my preference. I find myself tearing down rss fields I spent a lot of time building, because I want more people to train as troops. 

Hopefully, you kept relic hunting after your 2nd City and rolled right into your 3rd City. This is where you want to start rune crafting for maximum benefit. Tier 4 troops are mean and take a long time to train, so you need as many barracks as you can and keep homes down to only 3 or 4. Keep this city lean and mean. Only 1 of each rss field, fully runecrafted. No other rss fields, no embassy or watch tower. Build a Vault at first, but only level it to maybe L4 or L5. Build an Academy and do all your L10 research topics there. After you're done with all your L10 research, tear down your Academy and build a barracks. Same goes with the Vault.

Try to farm from your new cities to help level up your heroes and keep your vault full of rss. Level up one hero as high as you can to build faster and then train troops faster when you're done. Always keep your training queues full and reassign troops to City #1 when they are trained. 

That's my basic strategy, or at least how I would have done it in hind sight.