If you have a mixed unit of infantry (say 4 DA w/Exarch, 2 S. Scorps w/Autarch, 2 FD) inside transports when one is destroyed, how do you determine which infantry units are affected?

Every transport unit has dedicated stands which are inside. normaly we place them along with them with the note mounted so the enemy knows they are inside. then the normal target- and casuality rules apply.

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Attrition is the proof of absence of Strategy

That's correct.

You should inidicate which transport has which units within it.  One of our players has a piece of paper with "boxes" that match up with his transport units and he places the transported models on the paper off to the side while they're being transported.

Others just leave the models beside or on top of the transports after every move and mark them as "transported".

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"EPIC: Total War" Lead Developer

Now living in Boston... any EPIC players want to meet up?

Or if you use bases for your tanks you can number the bottom of the base and before every battle write down which troop types will be riding in what numbered tank.

Helps it look nice and neat on the battlefield and no confusion. Besides, wouldn't want the enemy to unfairly target specific infantry types would we?  

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-Malakai

"You'll never understand how much watching other people's pain gets me off, hearing their screams and knowing that I have the power of a god." -Velvet Acid Christ

In UK circles it is often the position of the units relative to the transport that show whether they are 'mounted up' or not. So when inside they are both placed behind the transport, while if outside they are usually one one side or the other, or in front of the transport.

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"Play up and play the game"

Vitai lampada
Sir Hemry Newbolt

I overlap the bases of the troops onto the base of the transport to show they are being transported.

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http://www.troublemakergames.co.uk/
Epic: Hive Development Thread

This is also the system we use to indicate bases mounted up or not.

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Attrition is the proof of absence of Strategy

I either set them on top, or I pull them back to the board edge when they don't fit.

But to answer the question more directly, you can either track unit-to-transport individually using any of the methods mentioned or you can randomize it in some way as the question comes up.  It's the preference of the players and something that should be covered in the 5-minute warm-up.

If you get into a situation where it hasn't been directly tracked, then you have to come to an agreement with your opponent.  If you can come to some sort of reasonable agreement, great.  If not, randomize it.

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Neal