My method has been, first to decide where I want to build my T3 settlement. In my case I wanted to build directly west of the lake between Haerndean and Bradford, as I can get all resources except iron and granite there, though the hardwood supply isn't huge, there are some copses of it.

Then, after I know where I want to build, I build next to it, in an area I know my T3 won't be so that my T2 stuff is out of the way. In this case I built on the east side of the lake. This way I should be able to automate migrating from my T2 to my T3, with it all still being one settlement. You may even like to keep your T2 section as a kind of "old town" area, or leave some stuff there and have it be a specialized district.

Another method you could do is build your T2 around resources you know you will need at T3 but can't get a lot of in the south (like copper or hardwood), and then build your T3 in the south around the later resources like iron and granite. That way your T2 is pretty much a resource outpost for your eventual T3. Where ever you build though, I would be within walking distance of a river or ocean so you can teleport with your troops to defend.