I think I am in a similar place with this.
I had a partial meniscectomy past June. I was doing PT before the operation(which was really helpful) and continued as soon as possible straight after.
All was going very well and after 4-5 months felt strong enough to start the 24-week program from this site.
I incorporated the PT into the general strength workout. So I was doing the core exercises for warm up as suggested and then did the strength with the PT guidelines(for number of sets,reps,etc). The thing is though that a lot of the exercises I was doing as part of my PT are same as in the strength work out.
For example I was doing box step-ups, lounges with barbell (which is the split bench squat), squats,etc so it was very straightforward.
After my last session with PT where she suggested I should keep doing 1-2 strength sessions per week I moved to following the book guidelines for these exercises.