Full Use Case: 
I would like to have one checkbox field shown on my custom object “Job” (labeled as AVTRRT in merge field code) and if that box is checked under field “Engagement Fee”, then merge 3 different conditional merge sections onto my generated document. Is this possible to do?

Yes, this is possible to do. Make sure there is a clear start and end to each of the sections: [SECTION_START:XXX]} and [SECTION_END:XXX]}. You also want to make sure that each section has it’s own name as you in below example with EngagementFee1, EngagementFee2, and EngagementFee3:

First Section
Second section
Third section