By side of your foot do you mean the the forefoot area?

Look on the binding box. It should tell you what size of boots are most compatable with your bindings. I highly doubt your foot will fit in a medium binding. Especially with as bulky as Burton boots can seem to be.

I am a pretty new rider and my knees get sore quickly, could it be the spacing of my bindings? what is the proper distance you should have between bindings?

there is no proper distance.  Eveybody rides what is good for them, you would know if your feet were too wide or too narrow.  dont be afraid to play with it. 
It could be that they are aligned improperly, like your stance angles are out of whack.  generally people like to ride between 5-18 turned to the front on the front and 0-18 on the back turned to the back.  The best way to do it is to jump with your eyes looking straight ahead at something ont the wall, for instance.  dont worry about your feet, and when you land look down.  The position that your feet are in will most likely be slightly flared (ducked) outward, and take this approximate stance to your board.