Adding extra axes to the input manager programaticly

I don't think so. You might be able to set up a number of "placeholder" axes which have no built-in meaning, and then change how your program interprets those axes at runtime.

Check out the script reference to see every documented function that you can call on the input system.

i realise this a bit late, but i'll reply anyway for people that have the same problem in the future. Check out : http://forum.unity3d.com/threads/130730-cInput-2.0-Unitys-custom-inputmanager-got-improved-!

This might just be what you need.