Read the section about the scenario icons and the ordering of cards. Similar to the original order of green->gold there are now specific icon for scenarios, so if you are playing X then you only draw the one with symbol X if able.
In terms of logistics I have added all the gameplay to the box in the third storage box just to remove the expansion boxes, but not yet integrated. My preference for the variety cards etc is to usually not add them until after my 5-6 session once things may feel repetitive.
