Need help optimizing routine-not sure if working out correctly and not seeing any results

Ok, so I have been working out somewhat consistently for 3 months. I have had to take a lot of weeks off, so 2 months of working out would be a better estimate out of all that. What I did in the beginning was work out all muscles every other day. I did that for about a month and a half, then switched to a day per muscle. At this point I did stuff like chest/biceps one day, shoulders/triceps another, legs/abs another. I am not fat (BMI 23.1), but I have a medium amount of pectoral and abdominal fat. I have not seen any muscle gains at all. Is it possible that the fat is covering the muscles and I actually did develop a little bit? I do kenpo twice a week for an hour but just started running 2 weeks ago 2-3 times a week for 2 miles, so I don't do a while lot of cardio. I just started using Cytogainer this week too. I am not sure also of the best way to do cardio, because I heard sprints are better for burning fat but I am not sure of the best way to do them and running seemed like more exertion. How can I improve my routine? I usually lift for 45 minutes on average, trying to lift weights that I struggle with in the last few reps of the last set so I actually build muscle. I can only get in the gym 3 days a week. Any help would be appreciated! thank you!