Actually, this is not normally an issue. Once you train yourself to type in a certain way, your muscles remember how to do it, even if you, consciously, do not.
At the other end of this, is the fact that because of muscle memory, switching to dvorak to fix a querty typing issue often does not solve the problem. (I'm speaking from experience here, because this is what I did.) Most people don't actively think about how they are typing, they type from muscle memory.
Instead, I found the best way to train myself out of bad habits was actually thinking about where my fingers are going and making a conscious effort to stem the bad habits. Re-train your muscles to type properly. It took me a few months of actively working at it, but I have had a fair amount of success with it, and now type properly with all fingers, and look at the screen when I type instead of the keyboard, or constantly shifting from the keyboard to the screen. It has helped a lot with my headaches, as constantly refocusing my eyes was leading to a lot of eye strain.