The old rule of thumb that thousands used was to ride rattrap pedals with your new shoes, no cleats. Mount the cleat to maintain that location. If you are placing your foot on the flats differently than your cleated shoes, maybe you need to adjust the cleats to mimic your flat position. (This would not work for me. I need cleats that force my feet to toe in to properly align my knees. If I don't do as my knees ask, I'll have to get new ones. But when I raced, people had been aligning cleats to their cleatless marks for 75 years. It worked for a lot of people.)