Rather surprisingly, this is not in the FAQ.
The answer is option "2". You place the hits on each transport and then resolve them as as you would for normal shooing or assault, with saving throws for the occupants
Quote:
1.12.7 Work Out Result,
(2nd para)
In addition, the losing formation suffers a number of extra hits equal to the difference between the two sides’ result scores. There are no saves for these hits, which represent units being hacked down as they turn and run, or disintegrating into a panic-driven rout as they flee. Remove these additional casualties as you would hits inflicted in the assault phase (i.e., units in base contact first, then those closest to the enemy, etc.).