Can you tell me if there are natural ways to deal with the pain of a foot amputation?

Phantom Limb. It is quite common for amputees to experience sensations on the removed limb. Many times it is pains, for others, it can feel different (itching for example). A study reported in nejm found that using a mirror to 'visualize' the removed body part actually helped resolve those sensations. http://www.nejm.org/doi/full/10.1056/nejmc071927. No matter what, discuss things with your doctor or surgeon.
Yes. Phantom limb pain can be problematic for many patients with an amputation at any level. I recommend these to my own patients with phantom limb pain. - stay active - find distractions when you are having phantom pain - mirror therapy. A 2007 study published in the nejm found that using a mirror to visualize and move the un-amputated limb reduced pain for patients in their amputated limb.