Flight A will warm up on the first event. When they are done, they will compete on the equipment they warmed up on while flight B warms up on the second set of equipment. After Flight A is done competing, Flight B will compete on their set of equipment (as they will be done with warmup) and Flight A will rotate to the next event and begin warming up on the Flight A equipment.
The only event this can be different on is floor. Sometimes with 2 flights they have 2 floors, sometimes they only have one floor.
If they have 2 floors, nothing changes.
If they have one floor, they can choose to have the B flight warm-up between the routines of the A flight. The makes it so you aren't slowed down by just one floor. At my daughter's state meet they had this set-up (2 sets of everything but floor) and only the very first flight had a blocked warm-up on floor. Every subsequent flight warmed up between the flight ahead of them.