Hi,
You could try setting the preferred angle for the joints.
To do this:
Delete the existing IK handle if it has one.
Select the knee joint, rotate it so it bends the right way. (Amount of rotation doesn't make a difference, just so long as you rotate it)
Hold down the right mouse button over the selected joint, and choose 'set preferred angle'.
Set the joints rotation back to 0, and apply the IK handle.
If you want to move a joint after it has been bound, you can try the following:
Select your bound mesh
Go to Skin > Detach Skin > Options. Make sure you 'Keep History'.
Now you can move your joints as desired, without it affecting the mesh.
Then, select your joints, shift select your mesh and re-do the smooth bind.
The weighting should have been saved and re-applied.
P.S - To move a joint without affecting it's children, hold down 'd' whilst moving it.
Hope that helps.
Good luck!