Thanks Mike.
Sorry, you're right, I wasn't very clear.
Basically I have a Futaba R6208SB S-BUS receiver which I am using on a multi-rotor.
I have one of the outputs from this receiver going to an Arduino MiniPro which is programmed to detect the PWM signal and use an IR LED to control a Sony NEX5 camera. This works very will and I can switch the camera modes between video and stills and take manual or automatic interval pictures.
As this is connected to one of the main outputs of the Rx and I have a Futaba 14 channel Tx (T8FG), I would like to move auxiliary functions such as this to the S-Bus.
So the code on the MiniPro will read the S-BUS and perform a function (either servo based or logic based) on say 4 channels.
I know this device (FUTM4191 SBD-1 S.Bus Decoder) is available to decode the S-Bus signal to PWM, however I would still need the MiniPro to perform certain functions, so I was looking at cutting out the middle man if possible.
http://www.futaba-rc.com/sbus/
I would need to define the channel on the MiniPro which corresponds to the channel on the Tx, for example channels 9 - 12.
Does that make sense or have I made it worse 
Steve