I have this figured out mostly. It appears there isn't very much specific documentation on performing more complex queries with a custom query option. I was originally using a stored procedure I created, but then decided to strip everything down and start all over. 

In my attached screenshot, you can see how you can get output values from a SQL query (or stored procedure). In this case I wrote the entire query in the workflow custom query activity to eliminate any issues with talking to SQL from workflow. 

One thing important to note, the columns "intakeID" and "intakeguid" both have default values in SQL; intakeID is an identity field, and intakeguid has newID() as it's default value which creates a unique guid.