Are you planning on maintaining your training program with the clen or focusing on recomping? I'd focus on cardio, shorter rest periods, supersets, etc for a while and bring the clen in when you are close to your goal. Really I'd get as far as you can get without it then bring calories back up for 2-4 weeks and then start your recomp again and add clen then.
Clen can be ran quite a few ways depending on goals and time lines. One way, when people have 20 weeks to prep, is to run it the last 12 weeks with Ketotifen or benedryl and a ramp in dosage. Another more common is 2 weeks on, 2 weeks off. I'm not a fan of clen, though I've used it numerous times, as the small direct benefit isn't worth it imo. I far prefer ECA or even albuterol, or something to help bring up my training performance.
Do you have pills on liquid? If you stay with clen then depending on goals, complete training, and time line would dictate how to do it. Assuming a 2 on, 2 off would be best: I'd start at 50mcg a day and increase 25mcg a day until you get to 100mcg-125mcg a day, cut dose in half last day and take 2 weeks off. Once you have your tolerance on mcg/day I'd hit half that the first day, 3/4 the next and then full dose for the next 2 weeks and repeat. On off weeks you'll be a little flat and that can effect mood, perception of strength, etc. It can be good to hit pre-workouts, caffeine, etc during that time. Clen is far from healthy and can cause permanent cardiovascular damage, and running things on off weeks only makes it worse but if results within a time line are needed then make your personal sacrifices as desired.