GFCI's on BLACK/RED dual 15-amp circuits
To start with, this is a shared neutral aka multi-wire branch circuit. One rule of MWBCs is that neutrals must be pigtailed when the other hot is near; you can't daisy-chain neutral through a device like a receptacle, because that would sever neutral for the other side if you removed it. 

Keep in mind on a plain recep, all screws are LINE.  There is no LOAD on a plain recep, because it doesn't do anything special like provide GFCI protection, dim, etc. 

If you leave the warning tape on the LOAD terminals and don't use it, then you don't have any worries about GFCIs tripping from miswiring.  The only time you'd get in trouble is if you did that thing with daisy chaining neutrals, that thing you're not allowed to do anyway, and tapped a recep's LOAD terminal for that purpose - in that case, you are correct, the GFCI would have a problem with that.  

 However, there's a safer way to wire your dock

Delivering GFCI protection at the socket is better than nothing, but there are all sorts of wire failures before the receps  that could leak current into the ground around the lake.  And many miswirings could cause the same effect.  

Further, outdoors is a terrible place to put a GFCI device; they fail all the time there.  

So you are actually better off fitting a 2-pole GFCI circuit breaker back at the service panel... And then you don't need any additional protection dockside.  The's no need to put a GFCI on a GFCI.  This will protect the entire cabling run, as well as all wiring dockside.