I have set each up in the environment to have only one channel activated (channel 5 for the Edirol keyboard and channel 12 for the TF)
Please be more specific about what settings you have made so we can set you straight.
You probably activated just those channels in the Multi Instruments. All that does is make it so you can only create tracks for those channels in the Arrange window.
Anyway, that doesn't answer your question.
To do what you want, you need to use 'multiplayer' mode.
This is described on page 122 of the Logic Pro 7 Reference manual.