It seems like you have already been doing most of the high intensity interval training with BJJ and Muay Thai, and that is one great way to get rid of your belly fat. However, here are some rules to remember when it comes to losing belly fat and gaining muscle mass at the same time:
Watch your diet closely - make sure to cut out as much sugary foods as you can (candy, juices, snacks, etc.). I believe studies suggested that men should consume about 30 grams of sugar per day and women is about 20-25 grams. In general, we already consumed much more than the recommended amount with just eating fruits and vegetables along with our daily meals. Next time, try to count the sugar contents in all the foods that you will consume, and you will be surprised of how much sugar is in your diet.
Next is to hit the abs effectively. I mean, you need to do some sort of an ab workout to really bring the washboard abs out. Studies have shown that these are some of the most effective abs exercises (stability ball rollout, single leg planks (front and sides), plank cross-over mountain climber and stability ball V-up). You can find these exercices on youtube.
To gain muscles, you must lift somewhat heavy. I mean you need to make sure that there is a consistent weight training program (2-3 days per week focusing on hitting the major muscle groups like chest, thigh, butt, back and core), and to make sure the volume and the dosage are relatively heavy (8-12 reps from your maximal effort). Try squat, benches and lat pull-down next time when you are at the gym. And if you are worrying about putting on too much weight with heavy lifting, you won't if you continue training with BJJ and Muay Thai the way you have been training. If anything, lifting heavy combining with your regular regimen will make you look more lean and toned.
Last and perhaps most important is to make sure you consume enough carbs and protein, not just protein. Your body will need most of the energy that is readily available first to rebuild, and that is carbs, not protein. Try to consume some of these foods from now on: peanut butter, sweet potatoes, avocados and whole eggs.
By the way, you said sometimes you run for hours, but the real question is for what? Unless you enjoy running for hours, new studies coming out supporting the benefits of high intensity interval training over long periods of slow and steady cardio training. I think a good comparison is to look at the sprinters and the marathon runners and ask yourself this question, "Who do I want to look like?" And then look at their training regimen to see their results. Try interval sprints from now on instead of long duration low intensity cardio training and start seeing those abs popping out.
Hope this has been helpful for you.