Once I upgrade the mastercode to v.6 to work with the autonomous libraries do I have to downgrade back v.5 to use the vex starup code?
No, the Master Code version 6 is all you need. You do not have to change back to version 5.
Is there a document that details the updates and/or changes between the different versions of Master Code?
No, there is no document that details the changes between the different versions of Master Code. You should always use the latest version of Code that we have published.