The way I did it, is to make 1 UVMap for baking to, and one for each texture you're going to use:

In my case, the rings uv map is mapped onto the appropriate texture, the bark uv is mapped onto a bark texture

Now in Cycles the nodes look like this

Using an Input>Attribute node we can type in our UV Map name exactly as it is in our UV map list. That is then connected by the Vector to the Image Texture we want it to be. So Rings to a Tree rings texture,

bark to our tree bark texture in this case. Each texture is set to clip, and each color is connected to the colour input of a seperate Diffuse Shader, then those two Diffuse connect to a Mix Shader, then output

Make sure for baking that you add in your seperate Image Texture node and assign it to the image you want to bake to. Make sure your baking UV (UVMap in my case) has the little camera next to it and you should

end up with something that has two textures on it like so:

::Plurk Frontpage Promotion::

I hope this helps someone else, it's been a thorn in my side for a while, and a lot of tutorials didn't help me figure it out!

OHHHHH I've always been wanting a way to do it, this will definitely come in handy

annettev: I bodged it a bit by making my bark textures 2048 and better tiled so I could put that on clip too, YMMV depending on texture