Practice, practice, practice - any some shorter water bottles may help.
My frame is very small, with compact geometry and I've found the only bottles that fit it comfortably are the small size Tacx bottles. They hold just as much as a regular small bottle, but they are a hair shorter and fatter so they fit under the top tube without hitting my rear brake cable - makes them easier to pull out of the cages without hitting the frame too. The only drawback is that they don't have any indentation at the top so they can be a bit harder to hold onto with long finger gloves on.