There is no requirement that you have one master keyboard. There are sixteen MIDI channels for a reason. Just have the pedal board send on a different channel than your master keyboard. (And if your master keyboard is sending on multiple channels due to splits, whatever, just choose a send channel that your not using.) The only problem you'll have is if your master keyboard is sending on all sixteen channels.
The issue is that you've got two (or more) sources of MIDI data, and you're going to want to merge them together before sending them to the audio generators. (That's assuming you aren't going to have a dedicated audio source for the pedals, and a different dedicated audio source for your master keyboard.) So you'll need to look for a MIDI merger. They're not that expensive.
If you've got dedicated audio sources for each of your master keyboards, then you've got no problems at all other than the cost.