https://bareknucklepickups.co.uk/main/downloads/schematics/general/humbuckers/2_hum__2_vol_1tone__3_way_toggle.pdfyou do it like this. The 3 way toggle is connecting either or both pickups to the tone pot and output jack. you only need one cap.
The way it works is that the some frequencies over a certain point will find it easy to pass through the cap, while lower frequencies don't. The pot itself is a variable resistor that keeps the cap away from the signal to some degree by making it tough for the audio to get to it. If you turn the pot down (less resistance between the signal and the cap to ground) then more higher frequencies can get through the resistance of the pot, then skip to ground through the cap while lower frequencies will still struggle.
A smaller value cap raises the point as which frequencies will be attenuated and vice versa for a larger cap.
you can think of it like a corridor. the narrower the corridor is (smaller the cap) only the thinnest people (higher frequencies) can get through. If you make the corridor wider then more average sized people can get through, bigger people might squeeze through, but some people will be so fat that they won't even try to squeeze through and they'll just go around (to the output jack).
so you can play with values. .022uf, 0.33uf, .047uf and see what you think. Other people here will have more of an opinion on the effect of the value.
Also, the material used in the cap can have an effect. Polypropylene Vs Paper in Oil. I've used the BKP paper in oil cap and it sounded nice. However I don't tend to use the tone control much and I even removed it from my PRS CE. So I can't help much on that front
EDIT: looking at that PDF, I think there is a wire missing from the back of the tone pot to either of the volume pots, otherwise the tone pot and guitar bridge isn't grounded.
