How does a System Repair Drone choose the order of repairs?
Solution 1:
According to one of the wikis, the System Repair Drone "Gives System and Sub-System rooms priority, repairing rooms in the order that they were damaged."
Solution 2:
Expanding on @tugs answer
There is no way to direct it to a specific room, other than sending it out multiple times.
So for example if your weapons room was hit first and then your FTL drive, the system repair drone will fix your weapons system. Another example, if your doors system was hit first and then your FTL drive, the drone will then go to the FTL system room first.