Do this:
Take the calipers off the rotors and push the pistons all the way in and clamp them there. Fill the master to the top. Start on the right side caliper and attach a bleeder hose to the bleeder screw and have it collect in a small bottle. (I highly recommend going to an auto parts store and getting the cheap one man bleeder bottle kit since it also has a check valve built in. Usually only runs about $10.)
With the bottle attached, and the bleeder screws closed, master lid off but full of fluid, pull the handle very slowly to get that air bubble out of the return hole. (It should only take about two or three slow pulls.) Put the lid back on the master. Pull the handle all the way to the grip and hold it. Crack the bleeder screw a touch. (You want to begin to see fluid just run out the caliper and fill the hose.) Close the bleeder screw and let go of the handle. DO NOT LET THE MASTER CYLINDER GET BELOW HALF! Keep doing this until there is no air coming out. Once there is no air on the right side, pull the handle until it gets firm and only crack the bleeder enough to check for air but not enough to allow the handle to bottom out.
Be sure to keep topping your master when it gets halfway down. (If done correctly, you will have topped the master at least 3 times by now). Switch over to the left side and follow the same procedure. Remember, the pistons need to be clamped in place the whole time. Once you are satisfied there is no air remaining, you should be getting a solid handle now. DO NOT UNCLAMP THE PISTONS UNTIL YOU HAVE A SOLID HANDLE.
Once a solid handle is achieved, install the right caliper with the new pads. Pull the handle slowly until the pads touch the rotors. Add fluid. Install the left side calipers and do the same thing. Top off the master after the pads are seated against the rotors. You should now have a fully flushed front brake system with a solid brake handle.