Can a DAC sort out a flat\cold amp?

there's something wrong, but truly should not be that amp unless it is defective.

to isolate the amp: skip the pc, make a simple direct path: a cd player directly to the yamaha to your speakers. a few familiar cds. 

great? lousy? then the amp is defective, who sold it to you?

Since your PC is the source keep what you have and do the EQ on the PC 

I doubt it is the amp. I would recommend a separate streamer… Bluesound sell budget streamers that are very well regarded and sounds like it would be in your budget.

I have never had luck treating symptoms (equalizer). I recommend going for the source of the problem. You can clean up multiple problems at once. PCs are very noisy and transmit that through the signal chain. A purpose built streamer avoids all of this. I tried all kinds of PC, Mac, laptop solutions and didn’t really get anywhere until I bought a streamer.

Get rid of the Scarlett and get a proper USB DAC like a RME ADI2.

Someone asked you to name your speakers and you didn’t tell. Is this a secret?

Without more info like speakers and pics of your room it is all guesswork and a waste of everyone’s time.

If the boombox sounds better, there are much greater problems here than the Yamaha.  The Yamaha is showing you the problems elsewhere.

Not to insult the OP @orenm145, but are you 100% sure that both speakers are the same phase? It sounds like your woofers are out of phase. What you describe is not an amp unless it is broken.

I would swap the wires from + / - on one set of speakers to be absolutely certain.