Hi Sam,
At Quintiq we are using VoIP for our audio and USB headphones with microphones for our presenters. For us, this works best as the audio via telephone line tends to break down quite often and it doesn't allow for multiple presenters (and organizers/moderators) to be in one room at the same time.
In the webinar tool that we use (GoToWebinar from Citrix), we simply mute the speaker(s) that are not presenting at that moment, and in combination with the headphones the audio doesn't interfere.
I hope this answer helps.
Best,
Stephan