Documentation will be updated after Scripts Organizer version 3 is released.
With Sandbox Pro you can have more than one Sandbox Sessions. Just hit the "Add New Session" button and create more of them.
Use the radio button to switch between Sessions.
There is no risk of conflict there.
You can risk-free start working on one session. Jump to another. Do some changes and then go back to the first one.
Every session is an isolated environment from a live website and from another session.