I'm with Chad here. I see agility as more of a coordination-training question. If you want to become more agile, do things that require agility: agility ladder work, hopscotch, precision drills, ballroom dancing, that tire drill thingy that American football players do, etc.
As to how to design a plyo workout, my guess is that Steve's "How To..." would be a good starting point.
My personal feeling is that an all-around athlete should have both: endurance and explosive power. There is a point of diminishing returns, of course. If you go too far one way you will lose skill in the other area and vice versa. But if you are well balanced in both, you will be more adaptable, although not necessarily outstanding, in either. That said, being competent and balanced in both will make you outstanding as an all-around athlete, if that makes any sense.
I guess my main question is, why are you interested in plyometric training? I don't directly see the relationship between plyo and agility. And if you are concerned about training for endurance, I don't think plyo will "hurt" that so much as simply detract from training time that you could be using to work on endurance.