rather than backing up the broker-guar and -pers files you can use the broker_load and broker_save command line utilities.
The storage files will backup all brokers running on the same enterprise server instance whereas broker_save will target a specific broker.
You can also export from the EI (VI) into adl files. There are specific rules that describe what is exported for each type (Integration Component, Integration, Configured Operation, Operations, Adapters, Document Types, and Document Scopes). There is a GEAR document that covers some of it and gives you an idea of the complications involved.
If you use ATC you have to export the blueprints and rulesets separately into xml files using the flow_architect. Keep in mind that you have to re-generate all the rulesets after you have imported them into a broker (Annoying hassle that takes about 8 mouse clicks per ruleset).
As you have gathered by now there is no way to effectively do version control for WM Enterprise Integrations if you use the WM development tools.
If you use ATC and java workunits then you have the same control you have over normal code. Adapters will still be configured using tools.
If you learn a more efficient method, then please share. This is one of the limitations of WM and their tools.