First thing you should check is your saddle hight and position. A seat that is too high or low, to forward or back, will adversely affect your pedaling. Personally, it's doesn't should like a big deal. A lot of times, I bring my knees inward when pedaling down hard on a climb, or too increase my aerodynamics going into a headwind. You can consult various books on training and see what top pro riders and coaches reccomend in regards to knee position, but still, it all begins with making sure you have the proper position on the bike.