Will Aux Output Use Up All Amps

It depends on the transformer, but in general, aux power will affect the total power available.

The questions are not the same, many transformers will rate the AUX power maximum far below the total power available, the MTH Z4000 is one such example.  On most PW transformers, the AUX power is drawn from the same windings as the track power and will certainly affect the total output.

How about being more specific as to the transformer and the AUX load?

The Lionel TW is also an exception, it has one transformer core with dedicated fixed taps, and another with combination variable & fixed, with about 4.5-5 amps continuous available from each.

Correct Rob, which is why I said most.   I used to have a couple of those, very odd ducks!

The Lionel CW80 has all 5 amps available, shared, from any combination of the track/variable posts and the Acc/programmable posts.

Right again, but using 3A from the aux will still reduce the track power to the remaining capacity.

I always recommend a separate accessory transformer unless there's a good reason not to use one.  For the small price of the transformer, these questions simply don't come up.

The reason for my question is that I bought an 80 watt Atlas transformer to use for aux power only in conjunction with one of my MTH z1000, so as not to rob track power from the z1000, but if all amps are not available through the aux, I may need to combine full open track with aux to get maximum amps.  Thought maybe aux would not deliver maximum power.

On the Atlas/Williams 80 watt, all current is available to the accessory taps. This is an "old school" wire wound multiple tap secondary transformer, with the train and acc wipers running across the same secondary just like a ZW(actually more like a Type R or SW).

The "train" posts are 0-18 volts, the "acc" posts are 0-16 volts.