"I was wondering if there would be an issue with putting a 9 frame honey super on tip of 10 frame deep supers. Since things won't line up perfectly, I was curious to know if it will cause problems. If so, can I switch my deep supers from 10 frame to 9 without it affecting the bees to much?"
no issue. i run 9 frame deep brood boxes and 8 frame honey supers. like perry said if you are starting with foundation, use 10 frames, and as soon as they are drawn, pull one out. also, just make sure to evenly space the 9 frames.