I also don't know much about the non USB pedals, but most people seem to have the same problem when attempting to set up the toe brakes with USB.
Many pilots get confused with the assigning of the x and y axis for both brakes and sticks. Remember that these x and y axis are different for each stick. As a result when you check the pedals to assign axis you want to have the rudder assigned to the z axis as you must know, but make sure you are also assigning the left brake to the pedal control to the x axis input. Then make sure you are assigning the right brake to the pedal control to the y axis input. A lot of pilots fail to check and assign these x and y axis, because they confuse these x and y axis with the x and y axis on their sticks. These are different and should be assigned to the pedal brakes.
The other big problem is that pilots forget to move the toe brakes fully during calibration. Remember to move all axis during the calibration routines, and that includes your toe brakes.
I hope this helps, but if it doesn't make sense let us know.
Ranger Bob