Having just switched from riding with plain platform pedals for three months (different bike), I find that pedals with clips feel odd beause very little of my foot is actually on the pedal. Mind you I'm a size 13 but I feel essentially like I don't fit into the clip because only 1/2 or maybe 1/3 of my foot in on the pedal and in the clip. I feel like I can't put it in as much power because I keep having to, with my calf muscles, keep my foot from flexing. Any suggestions or is this just how it feels and having the ball of my foot in the clip should be what I want anyways? Thanks.

what size clips you running?

Get stiffer shoes or go clipless.

i learned as a wee cyclist that the ball of your foot should be directly above the pedal spindle. if this is where your foot is with clips, you may simply be adjusting to "correct" foot positioning. it all depends on how you were riding without clips. I seem to recall that learning to use clips was a process of getting used to having my foot a bit farther back on the pedal. Without clips, one is prone to mashing down with the middle of the foot, or at least the flat of the foot just aft of the ball, for maximum stability/pressure. With clips, one has the advantage of the clips for stability, as well as the additional power of the upstroke, which negates the need for such uncivilized mashing.

however, it sounds like your clips are too small.

They are medium/large. I probably could find larger though I think that this does position the ball of my feet of the spindle (I'm gonna check) in which case I'm just whining about the feel of it. As long as I know it's where it should be I'm fine. Thanks.

They do make XL's for size 12 and above. And correct, the ball of your foot over the spindle.