I have looked for a while and I am wanting to understand how to manipulate the bones in an ogre xml animated model manually and from programming.
if i have too i'll get to the vertices and manipulate those, but i was hoping that there are some functions that I could use.
Yes you can. You can disable animation for a particular bone and then control it manually.
Check the test class jmetest.ogrexml.TestTurrentControl for example usage: