I’m honestly curious on what I should upgrade first to get better audio in general. Currently I have the Sennheiser HD560s and an Atom stack. I’m looking to spend about $500 on either a new dac and amp together or new headphones and a little later ill spend another $500 on the other.
If anyone has some recommendations on what I should do or what I should get it would be very much appreciated 
When it comes to spending 500 on headphones, it depends what you are looking for & where you are located.
You can get the Topping A90, it has received high praise and positive feedback. Violectric amps should also be in your consideration!
Get New Headphones now. Atom Stack is good enough for now and you won’t notice a big improvement with a sub 500 USD DAC/Amp for 560s (mostly sound signature change)
I’d recommend either the Sundara or Sivga Phoenix for Open and Meze 99C for Closed.
Save Up and get any off the following combos according to your preference
RME ADI 2 DAC FS
Schiit Bifrost 2 with Asgard 3 and/or Valhalla
You can also try Chord Mojo (with battery disconnected for desktop use) as a DAC into an Amp to see if you like Chord sound signature.
I say get a Little Dot MK2 tube amp (you can also pre-amp it to your Atom to get a different signature if you choose) and pair it with the Phoenix or Meze.
Personally and without knowing anything about your preferences, I’d probably try a planar like the Sundara.
WHAT are you trying to accomplish with the upgrade?
What would you change about the sound?
What is your usage of them, and do you see any new usages or opportunities going forward?