I am trying to set this up and there are two power connector bundles coming out of the Breakaway Box, each of which has a 6-connector and a 2-connector.
Do I hook up one 6-connector, both 6-connectors and one of the 2-connectors, or something else? How do I choose which connectors to use and which ones to leave hanging? There's nothing about it in either manual or that I can find via Google.
Are those two 8 Pin connectors (6+2) like it is mentioned in the Specs for your Sonnet Breakaway: https://www.sonnettech.com/product/egfx-breakaway-box/techspecs.html#techspecs
Those sound like the same type of GPU PCIe Power connectors that come with PSUs.
You can connect either just the 6 pin connector if the GPU card has a 6 PIN PCIe Power port or your can use the entire 8 Pins (6+2) to connect to your 8 Pin GPU PCIe Power Port.
This SuperUser Tech site explains it better: