Yup, 3.2 and 3.3 are for different situations.
In an engagement, both players roll all the appropriate dice (CC and FF, normal and MW (and TK) attacks) and total up the number of hits.
The opponent then allocates these hits as they see fit (whilst obeying the rules for hit allocation in 1.9.6), normal hits first and then MW (and TK) second. This is where Gorgons are fantastic
if they can get into an advatageous position.
So basically, if a Gorgon is in base contact with an enemy in an engagement, it can always be selected to take the first 3 hits that are placed (even if other DKoK infantry are in base contact as well).
One thing to note is that Gorgons (or any war engines for that matter)
cannot barge on top of friendly units to get to the front of an engagment. There must either be a clear lane for them to move between friendly units or they must be able to move clearly over friendly units (not easy with a 5cm countercharge).
Check
THIS THREAD for more details on War Engines and barging.