I will be assuming command of a squadron. Is there a transition guide that details the paperwork and other required reporting?

Congratulations. Check with your wing for guidance on specific requirements for unit commanders in your wing and region. In addition there are many resources available to help you be successful as a new commander.

If you haven't yet completed the Unit Commanders Course, please do so. It is your primary source for getting your head around the job. If you took the course prior to April 2017, consider reading the new materials released in 2017. It is quite different and more practical. You can find it on the CAP University page at https://www.gocivilairpatrol.com/members/cap-university/2017ucc/ 

Additionally, a new "Just in Time" Workbook for New Unit Commanders has just been released (CAPP 40-2). it'll offer a lot of help too.