What is the best way to use the jump squat? Should it be used in the same session as a regular suats in place of? What % of 1rm? Do you do them like a plyo jump or do you reset yourself each time? How for down do you go? etc? Any feedback is appreciated.
I think it depends largely on what phase you are in, volume and type of other plyometric exercises you are doing and also the events you are targeting.
I find jump squats beneficial and do them after short speed/accel work as well as split runs.
An example of the order of intensity
4 x 60 meter lying start
3 x 30 meter standing start
3 sets of double leg bounds or sprint bounds or hurdle hops (bodyweight only)
3 sets of jump squats
2-3 sets powercleans * optional depending on how fried I am after the plyos/speed
2-3 sets front squats
2 sets snatch grip deads
hypers etc etc
Even though the workout listed doesn’t look all that bad it is a pretty intense workout and requires training to get used to the volume and intensity.
As for technique I load about 25-30% of 1RM (95 pounds) and typically do sets of 6 reps or less. I do not go deep (probably between an 1/8th and 1/4 squat and try to be as reactive and explosive as possible. Jump as high as you can while maintaining miminal ground contact. Usually technique and fatigue can set in even after only 3 reps. If it starts to feel slower during the set stop right away.
I hope this helps, there are many ways do approach jump squats.
Cheers,
Chris
I use them together with regular squats.
Either before or together - complexed with the squats, altenratings ets, 2-3 mins between each --> the jumpsquats go higher, the squats go faster.
Don’t bother with % of 1RM, judge by how reactive you are when you do them, I rarely go over 45lbs. You want to be able to bounce up and down with ease. You could go heavier but that would train a different quality I think.
Poliquin says, 20% of a powersnatch, Russians say 20% of a limit Clean and Jerk, others say 15-20% or 30% of a squat —> er but what type of squat? 
I say go by feel.
I do both rock bottom and regular quarter squat style - depending on what quality I’m trying to train. Rock bottom ones are easier on the knees with heavier weights.
Sometimes adding a 10 sec isometric hold at the start of set at the bottom of the jump squat in either style.
I never do more than 5 reps, 3 reps is the usual figure.
Again you can reset if want to train a different quality. Each and every variation can and should be used. cycle em and the loads used.