Actually, Jabber and Teamspeak/Mumble are the big tools for coordination. Jabber for strategic communication, and Mumble/TS for tactical(Ventrilo is dead outside the smallest corps who keep on using Vent because that's what they've been using since they started...)
And yes, fleet commanders in these large battles usually have 4-5 voice channels active at any one time: Fleet commander group, scouts channel, capital ships group, supercapitals/titans group etc etc, and also speak to general fleet chat. Also maintaining an overview of spies etc, because a POS password might be changed etc.
In small-scale PvP, you usually don't have the same amount of channels, but otoh, you also don't have the same chain of command, so as a commander there, you have to keep track of more tactical stuff such as tactical target calling, keeping track of cyno use etc, which in a large fleet you have other officers do for you. Many commanders who shine in small-scale harasser group PvP can't handle commanding a large force, and vice versa.