It's really tough to walk the line between losing losing weight and getting more fit. I have been trying to do it for about 10 months now. The only advice I can lend is to try really hard to track your calories in and calories out as accurately as possible. Use these numbers to maintain a consistent but sustainable calorie deficit. I tend to find that looking at weekly net totals allows for more flexibility than trying to hit a daily goal. It allows me to take in a few extra calories the day before a big effort, and a few extra during/following that effort while still allowing me to stay in the ballpark with my weekly weight loss goals.

As I am approaching my weight goals, I have cut my deficit down to 3000ish calories per week from 7000 or so. I am definitely getting stronger at a faster rate now and feel like I am getting more benefit from my training. My weight loss has slowed to a pound every 1-2 weeks from the 6-9 pounds a month that I was running.

I track using myfitnesspal.com. It's the easiest tool to log with that I have found. The reporting leaves a bit to be desired sometimes but I really haven't found anything better or easier to use. Don't trust all of the calories burnt estimates given by them or any other site or device. Most are a bit high in their reporting. I am sure it varies dramatically from individual to individual, but I have had good results using a calculated BMR of a "sedentary" person using a couple of different methods and taking the average. I use about 80-85% of the calorie burn suggested by my HR measuring devices (Polar/Garmin) during exercise. Good luck.