If a 3 wire (multi-wire) circuit is needed then a two pole GFCI breaker is needed that has a neutral lug on it ( I think they all do now) other wise it is much lower in cost to run the circuit using regular breakers, (2008 require handle ties) to GFCI receptacles at the point you split up the two circuits into two separated runs with each having its own neutral from the load side of the GFCI receptacle.
You can always use a multi-wire circuit ahead of a GFCI device, but not after unless all current carrying conductors run through the GFCI breaker or device.