@Lady Chessa
The FS is awarded the points for each waypoint upon completion. Once the flag is taken for a stage, you cannot return to that stage and finish any incomplete waypoints; any badges that were in an unfinished waypoint are just lost. When going for finishing rank, it's important to get as many points as possible off each map before closing it out and moving to the next one. That usually means doing all the waypoints on all three maps*. There are 25,800 points available for all the waypoints on all three stages. The pits will run continuously until the end, or until the FS runs out of a badge there is no time left to make.
*There are strategies that involve determining the point value of the badges in the pit windows vs specific waypoints (for this FA structure, that's mostly in Stage 3). If the waypoint requires a significant number of a long term badge, the FS may skip that waypoint, opting to use those badges in the pits instead.