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How exactly does this work? If they can all fit in the fortification are they allowed to hold the same fortification?

Do you mean occupying the inside of a building? If so, only one unit may move into and occupy a building at a time.

Note that some fortifications (such as the Fortress of Redemption) count different sections as different buildings, allowing one unit to be embarked in each section.

I was thinking specifically for the aquila stronpoint which looks to have two/three different sections so can I have two/three units in it?

Some fortifications consist of multiple compartments / buildings for the rules. Each has his own "transport capacity" This is noted in the stonghold assault rules for them if it is the case.

 Spyro_Killer wrote:
I was thinking specifically for the aquila stronpoint which looks to have two/three different sections so can I have two/three units in it?

The Aquilla Strongpoint is a multi-part building of a large building (main part of the building) and a medium building (bunker annex) - page 110 of the rulebook lists the transport capacity and hull points for building sizes, as well as other rules for embarking into / disembarking from buildings.