which outputs do I use to a headphone amp?

do I connect the Apollo headphone outs to the Presonus inputs?

No, not really.

Setup depends on what you're going for. Different mixes for different musicians, ie, 2 way, 3 way etc. Whether you're looking at HP60 or HP4

The manuals give you a couple of setup guides and explains what each input and output is and does.:

https://www.presonus.com/products/HP4/downloads

https://www.presonus.com/products/HP60/downloads

If it's just you and no other musicians the HP60 may be a bit overkill.

How many people do you plan on recording at once that need headphones?

You can hear Logic out of the Apollo headphone out, right.? If it's just you the Presonus is not going to make the sound better, it's just gives you more headphone outs. In fact, the Apollo 8 headphone outs are quite likely superior to the Presonus.

I've said this a thousand times over the years... the most important part of recording is "you", it's not about the gear. First thing first, take care of business with the individual, educate yourself. Next learn the hardware, then the software, next record as much as you can. Recreate a track you like, study the EQ and compression techniques of the masters.

There was an individual in town who had a lot of money, he bought the best gear and hired the worst people, had no idea what he was doing... not one good track came out of that studio... along comes a talented kid with a 4-track cassette recorder and plays me one of the most impressive songs I've ever heard. Yes, this was 10-12 years ago but the point is always going to ring true, it starts with the individual.