The LC decoder only has 2 light outputs. They can be configured as headlights or to do various strobe effects. But it's an either or deal.
I have one in a SW1500, but I only have a headlight and a rooftop strobe.
Right now, Soundtrax really doesn't have any spectacular diesel decoders. You can deal with the LC series which I think sound pretty good but the motor control is not the greatest. Or you can go with the DSX and another decoder for motor and function. I did this in an Alco RS3, but programming is a bit of a pain.
The new Digitrax stuff would probably do what you want, but I'd listen first. Some folks are impressed with the sound, I still reserve opinion. I did one of the boards that takes the Soundbug. Easy install, great motor control and lighing effects, but the sound is much too quiet for me. Yes, the speaker is properly baffled.
Wait a few more weeks and grab one of the new QSI Revolutions that are supposed to ship in May. Great sound and it will do all the effects you want.