In the real aircraft it's all hydraulic. I mentioned a potentiometer on the stick for the benefit of my own sim project.
So, in the real thing it's quite simple: you squeeze the brake lever on the stick with pedals central, both brakes get applied evenly depending on how much you squeeze the lever.
While squeezing the lever, you push the pedals left / right, the aircraft hydraulics bias the braking effort from one side to the other.
If you release the brake lever and move the pedals, it has no effect on the brakes, only the rudder (if the engines are running for hydraulics).
To simulate this in FGFS you need two analogue inputs, one for the rudder bar, one for the stick brake lever.
The parking brake is applied by squeezing the lever, and rotating a catch on the control column to keep the lever in the fully applied position.
I imagine some gamers would have off-the-shelf USB / HID rudder pedals, but they'd need to tell FGFS to apply partial braking like squeezing the brake lever, maybe assign the keyboard "b" key to apply 25% braking, so when pressed in conjunction with the pedals would bias the FGFS braking? Keep "B" as parking brake on.
Hmmm - well, it's possible we could find a keyboard solution for less-than-100% braking, but I don't think its necessary.
For those with hardware, it's no problem at all - most flight sticks now have a dedicated "analogue" (mine have digital pots) rudder bar channel and a wheel brake channel could be assigned if required. If not, tapping B repeatedly (or a hardware button) while applying the rudder will have a similar effect to applying constant braking at, say, 25%. I suspect most people will opt for the "cheat" nosewheel steering to be honest anyway.