Hi @rrowlands.
We also have instructions here:http://opendatakit-dev.cs.washington.edu/2_0_tools/release/218/cloud_endpoints
I think these instructions should answer most of your questions.
However, I am a little confused by some of your questions. The Sync Endpoints are used instead of Aggregate; they do not talk to each other.
ODK Aggregate is used as a server to receive your records when collecting data with ODK Collect or another ODK 1 tool. You can also use ODK Aggregate’s Tables Extension to make it work with ODK 2 tools. In either case, ODK Aggregate is your server to receive data.
Sync Endpoints is also a server to receive data, but are ONLY comapatible with ODK 2. The will not work with ODK Collect. You can spin up a Sync Endpoint and send and receive records with ODK Services, Survey, and Tables (the core 2.0 mobile tools). The reason to use Sync Endpoints is if you want to take advantage of the latest features of ODK 2, like group permissions, or you prefer the use of a docker container.
ODK Aggregate and Sync Endpoints do NOT talk to each other. They each have their own database because they each receive records from ODK mobile tools, but you either use one or the other.
Are you using ODK Collect? Or the ODK 2 tool suite?