I'm using X52 HOTAS with a custom profile, Thrustmaster Cougar MFDs with my own custom software to send the appropriate commands to EECH and Saitek Pro Pedals. They all work great together. EECH has the ability to select the axes from any joystick attached to the computer, you just have to click the next/previous buttons enough times to loop through them all. It pulls the names from the joystick itself, so it will match the name in the joystick control panel, like X, Y, Rudder, Slider, Rotary on the X52 and Left Toe, Right Toe and Rudder on the pedals. There is no assignment for the toe brakes, so that is unused as is the Rudder axis on the X52 as I'm using the Rudder axis on the pedals.
The biggest thing I can say about the controls you use with the sim is it has to comfortable, configurable enough to let you get what you need out of it and not break in 2 years.
Oh, and I'm not using the saitek software for combining the rudder inputs into the profile. I'm only using it for assigning functions for weapons, nav, targeting and countermeasures while the MFDs handle the other controls needed for a good time.