I've got a Behringer FCB1010 that I've programmed to control my Fender Cyber-Deluxe. The programming interface is cumbersome, but once you have it set up the way you like it is great to use. Having two rocker pedals on the board is very handy and is much easier for setup/breakdown and transport than having to plug in external expression pedals.
The trick is to spend the time learning what MIDI control and program changes do and how they work, and similarly, what the MIDI capabilities of your effects unit are. Prepare to spend a few hours tweaking the settings between the two just to get the hang of how they work together. You will get frustrated, but if you actually get beyond that to understand what's going on it will be worth your time and effort. Once you understand how they interact, then spend some time designing your layout.
This is the key. A well thought out MIDI pedal board design is a joy to use. A pedal board that is poorly laid out and forces you to hit multiple button combinations to get from A to B is more trouble than it is worth. An hour of planning will save you many hours of headaches and re-working.
I've been experimenting with MIDI controllers and rack effects for years. The absolute best and most powerful foot controller ever made was the Digitech PMC10. Amazingly flexible interface, a great alphanumeric display and best of all a very clever user designed a great PC editor to program the thing. I used to design Mac MIDI editor/librarians for a living, and the PC editor for the PMC10 puts my own editor to shame. Sadly the PMC10 has been out of production for over 10 years and they are extremely hard to find. But if you ever find yourself saying "why didn't anybody ever make a MIDI foot controller that can do <blank>", they did.
And for full disclosure, I program the FCB1010 with the MOTU Unisyn editor I designed instead of doing the pedal tap-dance. Unisyn is a commercial product, rather expensive and currently not under development, so I wouldn't recommend it. I am no longer a MOTU employee though I still have lots of friends there.
-Jonathan