Prilepin's table is based off information/statistics of Olympic lifters and their training. So some people are of the opinion that when applied to powerlifts the number of total reps should be lower when training above 90%. This is because with the powerlifts (as compared to Olympic lifts) there is more weight being moved, the lifts take longer, and with the squat and bench there is an eccentric part of the lift. Although not follows this belief.
Prilepin found that lifters doing more than the perscribed reps per set either had technique break down, or bar speed decrease significantly, or both. The idea is to stimulate strength gains, not grind out as many reps as possible.
Then I'd recommend Bill Starrs 5x5 or Texas method. They have heavy days, volume days, and light days. The days are grouped like that to improve recovery. If you want something that makes use of Prilepin's table (while incorporating any number of other principles) you could try a beginner sheiko routine. If your knees and lower back are bothering you, deload for a week, and then, if you decide to do so, start a new routine.
Prilepin's table is a very good guideline, but you won't necessarily always follow it. Some routines may have you do less or more than the recommended volume, and less or more than the recommended reps per set (especially at lower intensities). And with experience you'll understand whether you generally need to do less or more total reps, and reps per set. For example, you might find you get overtrained easily, so you tend to do less total reps, or maybe you find that tonnes of volume works well for you, and you train towards the upper end or even slightly above the recommended total reps. But Prilepin's table is a good starting point, and it answers the question of "what reps, sets and intensity should I use?" very well.