(I'm guessing you mean the "ball" at the base of your big toe, not the underside of where your toenail is.
)
If the orthotics are making your foot hurt, throw them away.
I bruised the ball of my foot
(at the base of the big toe
) last year. It took a couple weeks for the pain to go away. Ice, ibuprofen, rest, and gentle massage all helped.
In my experience, with the right pair of shoes, you should not have foot pain that keeps you from running. A little pain is expected, but when it starts to border on injury, there's a problem. You might need a new pair of shoes
(go to a specialty running store
), or the pair you have might just not be the right ones.
For example, I take a neutral shoe, but there are a dozen to choose from. There's one shoe that really seems to work for me, so I keep buying that one. For whatever reason, whenever I try something different, I always have foot problems.
(By the way, it's an Asics Nimbus VI or VII, but what works for you might be different.
) Maybe you just need to find "your shoe".
Mike