We went to Amankila and Amanusa this March. Loved both beaches, but they are different.

Sand:
Amanusa has white sand while there is fine darker sand at the Amankila beach.

Bales/loungers:
Both great. I would say more or less same kind of bale and loungers, covered with lots of soft towels. Ice water, suncream offered in the bale.

Privacy:
The beach at Amankila is a bit larger meaning there is some more distance between the bales. There is, however, trees and green plants in between the bales at Amanusa, so they are private as well, but maybe slightly less private than Amankila.
Amankila's beach is really private and the only people you see except guests, are local fishermen sometimes. At Amanusa it is possible to walk over the beach as it is connected to other beaches at each side, i.e. you see more people walking by. Not a lot, but some.
A third point is that since there are so many pools at Kila, the beach might be less full there, i.e. again more private.

Facilities:
Restrooms, changing facilities and restaurants available at the beach clubs at both beaches. Slightly longer walk from the beach to the facilities at Amankila, but the facilities there are nicer and more comfortable. In addition the beach club restaurant at Amankila is more "covered" meaning that you can use it also if it REALLY rains (we do not want that, but still). Also, of course, you can use the beach pool at Amankila while on the beach - at Amanusa there is no pool at the beach.

Food
We had only simple meals like pizza or sandwiches at beach, so cannot really comment. Pizza at Amanusa beach was really good, though.

Water sports
Equipment (smal boats, surf boards etc.) available at both beaches. Did not use it, so cannot comment in detail. No snorkelling of the beach at any of them.

Service
Excellent at both beaches. Can have meals and drinks in your beach bale if you do not want to go to the restaurant.

Swimming
Waves and current was more noticeable at Amanusa when we were there - a bit hard to get in and out of water because of this, but OK to swim, but that varies according to wind and season I guess.

Getting to and from beach
Walk down, buggy up at Kila. Car both ways at Amanusa (see also below re car)

Others
Lots of little crabs and also a large lizzard spotted at Amankila. No "wildlife" at Amanusa.
Sometimes there are large tankers to be seen in the sea outside Amankila - might spoil view.
Building work close to Amanusa beach. No direct access through golf course with the cool cabrio when we were there because of this, needed to take a normal car through the village (not far, but not as nice as the alternative). No noise when we were there, but this can be a problem so check.

So - as you see - a bit difficult to choose.

If I were you, having only two nights, I think I would go to Amanusa since it will save you some transport time and give you more time at the beach, and then rather save Kila for sometimes when you want to do everything that this resorts has to offer.