EmmaNem98,
The snap, crackle, pop sound from the ankle is called benign crepitus. This is actually very common, as many people have the popping sound when they walk up stairs. In some people, it is so loud you can hear it from across the room.
There has not been any association of the benign crepitus with pain or other disorders in the joint. The crepitus can occur in any joint in the body, but people note it mostly in the knee, ankles, and fingers. Cracking the finger knuckles is a type of crepitus. We still do not know the cause of the sound.
However, that is not to say that the sound could not be associated with some problem in the ankles. But, usually, the sound and the problem are two separate things. Even if the other disorder is taken care of the popping may not go away.
But, as to your pain in the ankles and feet. Do you have the same pain when you run in your other athletic shoes? If not, the pain you have in softball may be coming from your cleats. Baseball cleats sometimes do not have the best arch supports and padding in them. Again, make sure it is not coming from your cleats.
If you have pain every time you run, no matter what shoes you are wearing, then it is going to be a little more difficult to figure out what is going on. It is hard to tell exactly what is going on, over the internet. You really need to examine the foot and ankle to get an idea of what the problem is.
Such as, where do your feet hurt? To say all over, really doesn't help very much. Exactly where do they hurt? Is it in the ankle joint, around the big ankle bones (the medial and lateral malleolus)? Or is it more in the arch of the foot? Is it more in the ball of the foot or the toes? Where is really important. Because that will narrow down what could be causing the problem.
There are a lot of things that could be causing pain in the ankles/feet in an adolescent. If you have a trainer at your school, you might ask him/her to take a look at your ankles. If your Mom doesn't want to take you to the physician, and you do not have a trainer, you might ask your coach or school nurse to take a look at your ankles.
If you can give a little more information, I might be able to give you some ideas of what might be wrong.
In addition to the above questions, do your ankle hurt any time else? Have they hurt like this before? Have you sprained or twisted your ankles in the past? What is the pain like, is it dull and achy lasting a long time, or is it a sharp pain lasting for only a few moments, is it burning in nature or electrical? Do you have any other symptoms, such as numbness or tingling, redness, warmth, anything? Anything else that might be of help?
So, again, if you can get me a little more information, I might be able to better tell what is going on.
Good luck.