Welcome to hifiguides!
What sort of help/advice are you looking for?
More details on what you want to accomplish will help 
Also, what are you focusing on? Headphone? Speakers? Music? Gaming?
I applaud your science based commitment to monitor ergonomics 
Hey @Bensnake088 - welcome to HFGF!
Certainly looks like you have some room to work with, and already off to a good start.
I see you met @elementze already so you are in pretty good hands already.
Let us know what you are thinking about and I’m sure there will be no shortage of ideas for you.
Speakers and Gaming i guess?
Is this a decent setup? I got these speakers from my dad and and amp with them and managed to hook it up but I don’t really know what I’m doing.
Is it fine to keep the speakers as is or would it be better to put them under the table or maybe be mount some shelves and put them there?
Appreciate any help and advice and suggestions
A stand or shelf for the monitor would clean things up a bit. If it can be vesa mounted even better
good news, we do that around here! 
The easy answer is: do you enjoy the way it sounds? Then it’s a decent setup
I’m only partly joking. Always be your own judge of what is “decent”. Everyone has different taste, budget, goals, etc. Be your own critic on what sounds good.
With that little bit of “philosophy” out of the way, tell us more about your gear. Speaker brand and model. Amp brand and model. Looks like some headphones there, again, brand and model?
If you don’t know what you are doing and got this far, you are doing okay by me!
It all depends on where you are listening from. Do you listen to the speakers while sitting at your computer? Or are you another places in the room when listening to them? Speakers tend to be all about placement: separation from each other, distance from listener, angle towards listener, distance from wall, etc…
Speakers are Sony SS-A 490 and the amp is Kawachi MA-D20. The headphones are Razer Kraken X
Mainly listening to the speakers from a chair.
Those monitors are substantial, push the left speaker further back to the wall, triangulate those bad boys.
I don’t have personal experience with any of these pieces. Doing a little internet sleuthing on the speakers:
Type: 3 way speaker system
Frequency Response: 50Hz to 20kHz
Recommended Amplifier: 100W max
Impedance: 6Ω
Sensitivity: 88dB
This is reasonably efficient and decent power handling.
One thing to check with speakers of “advanced years” is foam rubber seals around the speaker cones. They tend to disintegrate. (Just something to check.). Sound quality wise, hard to say. I know these specs are easy to match (and beat) with small, modern, dsp corrected speakers. But that doesn’t mean these are bad. If you like 'em use 'em. My personal issue would be size. They take up a lot of space, and likely sound best >6ft away. Speaker placement is never perfect, limited by room size. But these are pretty oversized for the space. Something smaller would likely sound better in the space. But again, be your own judge of sound quality.
Amp wise, this is a unique device you have! Lots of uncommon features (ie FM radio). It probably puts out enough power for these speakers to get loud. But again, it’s an older unit, you can match and beat it with modern gear easily. A good example:
Not saying you should buy this, or anything. Just giving an example.
So, overall, it’s a unique older setup. For a modest budget you could get a more modern setup that will match or beat it. But enjoy the music!
as long as you have the room, theres no reason to not use them. they are the previous gen of the current sony’s that lots of peeps love. and just because its old, doesnt mean it doesnt sound good. manufactures come out with new shit to sell. doesnt mean the old is bad.
that amp though…might wanna consider updating it. you can get better, cheap chifi amps these days. amazon has a ton of them below 100$