I like to do an easy 3-4 miles, then a circuit of plyos, followed by another 1-2 at 30-45 secs/mile slower than my marathon pace. The plyos build up a lot of lactate in my bloodstream, so those last two miles are pretty painful, but I think the experience of running while tired helpd me. I don't think there's a magic formula, and plyos do not seem to benefit some runners and/or lead to injury. My basic rule is that if an exercise seems to stress a muscle or joint, don't do it.
I follow some components of the Loughborough plan, which is a mix of upper body (push-ups, dips, pull-ups), core (crunches and oblique abs) and leg power/strength. Squats and aggrevate a knee I injured many years ago played softball, so I don't do them - instead I do lunges. Instead of knee-extensions, I do leg lifts, which also addresses my core. Bounding is also a little tough on my 41 year old legs, and I do not think they were doing much for me. Box jumps onto a rubberized surface are fine, and I think they have helped my hill-climbing strength. I also do single-leg step-ups, but instead of hip thrusts, I work my hip adductor/abductors on a machine and while I agree that jumpping rope is not very running-specific, a set gives my abs or arms a break.
So do plyos help? They certainly do not replace running, but they do help me burn fat and strengthen my core. The better muscle tone also keeps my wife from complaining that I look too skinny.