To start, you can run the Filter Pro rack just like you did the pedal version in the 3rd loop of your GCX. The rack version has 1/4-inch unbalanced ins and outs so there should be no problem there. MIDI doesn't carry any audio information, so...
Now, the main benefit to using MIDI in this case is whether you want to change presets ALONG with your GCX. This is as simple as just running another MIDI cable from your GCX to the MIDI IN of the Filter Pro.
I demonstrated this type of setup using a Commander to send program changes (which the Ground Control Pro does as well) to a Delay and Mod Pro. You can see this here: http://www.youtube.com/watch?v=2GJCw8w9 ... annel_page
As for the latency when changing presets in the Filter Pro, it's barely noticeable. You should be just fine.