you can really use any program that will fit in to a 2-3 day a week schedual. if your running m,w,f, and lifting t,tr,s then it would work out.
personally when I'm doing a lot of cardio i like to do either a 5x5 or a 3x5 to keep my strength up. Perhaps two or three days of fullbody workouts would work best. If your knees are taking a pounding from the running, dont forget you can do HIIT on a stationary bike, or a eliptical, or a rowing machine ... ect ect.
I don't do this for my family, my friends, women, accolades, pride, or ego. I do it for me and no one else, its just part of who I am.