Practice slowly and methodically. Read some of my articles on this topic in the 5-Minute Lessons. There's several on Kick drum control and development ... but also check out the Endurance Method and Expanding Stick Control for the Drumset.

Break down the beat/groove so that you can play just the hand parts, then the feet parts. Then try playing the Kick with the right hand part; next the Kick with the left hand part. Then put it all together.

You are having to use mucles and coordination skills that you are not used to using. There are no short cuts other than practicing and putting the time in to developing technique and coordination.

I also recommend that you try taking a few lessons from a professional drum instructor. They can help guide you in the areas that you need some direction or assistance.