In general, to add an extra circuit between a switch box and receptacle (fan), yes, you just need to add another hot (may be black) wire to run between the fan and one of the switches. The neutral wire (white or grey) is shared, and you can use the one already in the receptacle for both circuits.
If you want to add the extra wire, you will need to trace exactly which route the wire follows from fan to switch. Also trace any other circuits that use the same path of conduit. Power down these circuits at the breaker box, and use "fish tape" (stiff, flat, metal wire) to pull a new wire through.
The difference between a three-way installation and a normal switch, is an extra "runner" wire (typically red) between the two switches. They also use special three-way switches.
The remote control unit might be the way to go. This is what I suggest to my customers. If this were the case, you simply connect the fan-unit half of the module to whichever circuit is already in place (the switched wire from the fan box, and the white/grey neutral). The output wires from this module are labeled "neutral," "fan (hot)," and "light (hot)."
Hope that helped, good luck!