Such as an Engineering team on the fore and and another on the aft? Pretty sure you can't we're in the middle of a game and can't find anything online.

They are marked as limited, but i am not sure if that means ship or section.

It doesn't mention anything about "sections" in the rules so I would have to go with one limited upgrade per ship.

From page 4 of the Huge Ship Rules:

Limited Upgrades

Some Upgrade cards are labeled “Limited.” A ship cannot equip multiple copies of the same card if that card is labeled as “Limited.”

Such as an Engineering team on the fore and and another on the aft? Pretty sure you can't we're in the middle of a game and can't find anything online.

Need to find the rule that deals with limited cards.

I'm fairly sure it'll specify that limited cards can only be issued one to a ship, and since the Raider is listed as being ONE ship with TWO bases, that would restrict this usage.

EDIT: WWHSD Ninja'd the answer. Limited cards are one two a ship, and huge ships are still single ships.