Basically, it's all about the transitions in an intake manifold, as well as the piping size. The transitions are going to allow for the smoothest airflow, and the runner cross-sectional areas are going to allow for a certain air velocity. You basically want to size your runners for your airflow requirement at your top end. This amount may give you some weird peformance at lower engine speeds due to the lower kinetic energy of the flow going into the cylinders on the intake stroke. The momentum of the air actually continues to force air into the cylinder after bdc, and lowering the velocity of the air in the runners will decrease the air's momentum, and less air will be forced into the chamber. This btw is only really applicable to NA applications, as a turbo app would force air into the chamber regardless. You just need to decide where you think your max mass flow is going to occur, probably somewhere in the 7000 rpm area, and size your runners based on a calculated flowrate at that engine speed (you won't get exact, but then again, engine design is a LOT of testing to go with design, where your fluent would come in: in order to model it accurately though, you'd need to model a simple engine design, probably more than you are willing to do - parametrics will own you.).
The larger the plenum, the more even the flow will be likely to be across each runner. You can see this on a lot of custom manifold designs.
Just round the edges of the transitions, and you should be good to go. Do some screen shots of the fluent when you do it btw. I'll hopefully be doing a fluent model of my uav next month. Keeping fingers crossed.
Good Luck on the design, let us know how it turns out.