ok... now I am confused again.

When I added the second polygon as an influence object it worked fine. But when I went to adjust the weights on the polygon that I used as an influence object, a completely new polygon shaped exactly the same appeared underneath.

That can't be right. Am I supposed to just hide this new polygon as it is just an influence object? what am i doing wrong? There must be a way to add new joints to the influence box in the paint weights tool settings.

Anyone who knows what is going on please help. Thanks!