During this time of year jumps are done on lower body days after warm ups and prior to the Max Effort Movement or Speed Squats.
This is an early off-season example. These are not set in stone. When you set your program up have some thought and progression to the waves so you aren't just throwing random jumps into the program. This will help build a foundation to later support more intensive and true plyometric training.
Max Effort Day Dynamic Effort Day
Week1- Seated Box Jump 3x5 Week1- Box Jump 3x5
Week2- Seated Box Jump 4x5 Week2- Box Jump4x5
Week3- Seated Box Jump 5x5 Week 3- Box Jump5x5
Week 4- bring the volume down, increase difficulty - built in deload. Then progress the volume for the next 2 weeks. Ramp up for 3, bring it down on the 4th.
Max Effort Day
Week4- Seated Wgtd Footslam Box Jump 4x5
Dynamic Effort Day
Week 4- Single Leg Box Jump 3x5