How did you set up the cargo manager so that the cart returns when it's out of rails? A screenshot might help, sence I didn't use the cargo manager once and it seems like it has a complex interface...
Well, the cart will automatically return when it runs out and can't go forward. They are kinda smart.
As for setting up the cart manager...uhm, kinda hard to explain online. I know DW20 did a video of how to do it, but I believe it was in his SMP...so, could be hard to find. He probably also did a spotlight, but I don't recall how well he showed setting up the manager there.
I will try for a rough explanation of what things do though.
First, theres the icon box which sets what the cargo manager will interact with. Example would be the engine symbol tells the cargo manager it will be working with the engine, so it will load fuel.
Next, the colors indicate what side of the manager that particular interaction will occur on. So, if the above engine is set to yellow...only when the cart reaches the yellow side, will it attempt to refuel.
Then theres the weird sort of track symbol. You can have either a straight line, or a sort of Y. The straight line means after finishing with the given task it will continue straight. With the Y, it will turn around and go back the way it came.
Finally, I forgot how, but you can adjust the storage areas in the cargo manager to be connected or not in various ways. So, for example, you could just have 1 big storage. Or, you could have separate storages for each color.