For PWM audio a filter is recommended but not essential.
Most need hand making, see here:
http://www.sudomod.com/game-boy-zero-guide-part-5/
About 2/3 down.
USB Audio does not need a filter but it doesnt look like you have that setup.
Either way, to add in the headphone Jack, see below taken from Wermys second guide:
http://www.sudomod.com/game-boy-zero-cu ... de-part-1/
This explains the pinout on the jack.
Essentially:

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The pins for the headphone jack I’m using go (from left to right in the above image): ground, left channel, right channel switch, right channel, left channel switch. What I mean by switch is that without headphones connected, they are connected to their respective channel. So, you’d want your speaker hooked up to the switch pins, and your audio source (Amplifier) connected to the L/R channel pins.'
Ground can connect to your button PCB.
So from your setup i see this being wired as follows:
- 2x PWM Audio outs from Pi connect to the single Input pin on your 3 pin volume pot.
(Ideally use a 5 pin volume pot so the 2 PWM go to the 2 inputs (L + R) on the volume pot.
- 1x output pin on volume pot goes to Input on your Amp
(If you use a 5 pin pot, both output pins go to both input pads on amp)
- 2x Outputs on amp go to L and R channels on headphone jack
- L + R SWITCH pins on headphone go to speaker.
- Ground on your headphone jack is wired where you see fit.