How does the We communicate? Well, it communicates with you via the magics of the Amber College with a little help from some enthusiastic pedipalp gesture, but its internal communication is a lot more mysterious. You don't think you quite managed to communicate what it was you were trying to achieve, but they're happy for you to spend time inside their nest while they engage in their habitual internal communication, and you turn your Magesight onto the Karak's strangest allies.
It's easier said than done, of course. If their communication method was easily visible, you would have seen it already, and the We were unable to describe it without making the chirping noise they make when the translation magics fail. So after double-checking that there weren't hitherto unnoticed packets of magical energies flowing back and forth, you settle in to get a good, long look at their souls, which is also easier said than done. Magesight is often described as the ability to see souls, but what is usually seen is the ambient energies given off by souls, and the traces of Winds swirling about inside them. Seeing the soul itself is like trying to see the wick of a burning candle, both in difficulty and in likelihood to result in headaches.
The fundamental question you first seek an answer to is the nature of a We soul, and what you piece together over long days punctuated by headaches in your soul is that the answer is in a grey area. The We in their colony share a single soul, but it is a shapeless and amorphic one compared to that of the beings you're used to, and when a Hunter leaves a fragment of the greater oversoul breaks off to go with it. It's not dissimilar to theories you've seen referenced on the nature of the souls of other eusocial insects. So that means that internal communication via the soul is quite possible, and with the help of the bemused but cooperative We, you set to work testing for it. Which itself wasn't that difficult, because all it takes is a tunnel adjoining the Hall of Pillared Iron that the We call home, where a Web-Weaver carried in your arms rejoins the oversoul of the We but remains unmoving, as per the last set of instructions it received before leaving in the first place.
So, sound. Perhaps higher pitched than you can hear, perhaps lower, it doesn't matter terribly much. Either way, the We appear to be entirely non-magical, despite how alien they are from sentient life as you know it. You must admit a little disappointment that the answer is so mundane, but it does fill in the few remaining gaps in your knowledge of the We.