Can I do two circuits on 12/3 and still have GFCI?
This applies to all MWBCs

That type of configuration is called a multi-wire branch circuit (MWBC). In this arrangement, you connect a receptacle to one hot and the shared neutral. It is a Code requirement that neutral be pigtailed (i.e. don't use the receptacle as a splice block for neutral). The rule is to assure that neutral is not severed for the other half of the circuit. (this can cause all sorts of bad). 

This applies to GFCI on MWBC

You can absolutely install GFCI+receptacles at the beginning of the wall run. You just won't be able to use the LOAD terminals to carry the circuit onward - you will need to pigtail both hot and neutral.   Because you can't use the LOAD terminals, only  those receps will have GFCI protection - you can't pass it downward to the remainder of the MWBC.    You'll need one GFCI per outlet that you want to have GFCI protection.  

If you want to GFCI-protect the whole circuit in one shot, use a GFCI breaker at the start, then plain receps throughout. .  Mind you, the circuit may require AFCI also, in which case you'd use a GFCI+AFCI breaker.