Ehr...
How come I can add mods/Add-ons to an excisting save by activating them in the main menu and then loading the save?
this is a bug

We want to separate regular modding logic from GM sessions logic. This will be fixed soon, and then we will provide manual way to select and plug-in addons to active session so mods for main campaign and for active gm sessions won't be overlapped
Do you just load up the campaign like you ate playing without the players logged in to keep adding scenes?
Yep, play mode has same set of functionalities as a prepare mode. So you can just load saved session and continue working on it. Only difference that changes you will made won't be reflected in campaign you prepared before and you will already have player characters. I.e. when you starting a session with some campaign - you creating a copy of that campaign and using it for your session.
This is done because every session can go different way based on the player choices so it could be that changes for one session are not needed for another