Hi Paul - You can get a switching relay that can handle multiple zones, look up "Taco SR503-4" to see an example. As for the piping, you can pipe all three zones in a primary/secondary fashion, but it really isn't necessary. On my dad's system we just put the zone circulators on a normal boiler header, but the zone feeding the radiant floor was a mini primary/secondary setup...like this:
Basically there is a short loop from the circulator back to the other boiler header, with two closely spaced tees on the loop...the two tee's are the "secondary" loop that feed a second circulator and mixing valve.
There are different ways to pipe and control the boiler, some more expensive than others. The big thing is to make sure the circulators and piping are sized properly for the loads they serve.