If you are sending the AC3 track via MPEGTS then this is just pass through to the end clients that support AC3, no transcoder is required. If you are using an RTMP encoder to Wowza then this is more of an issue as this probably will not work without further investigation. I think there is a RTMP code for the AC3 codec but not sure we would support it at the moment.
There is no need for any special configuration when using MPEGTS as it will see the AC3 codec and pass through the data.
As for pitfalls, none that I can think of, but as there are many different types of encoders it may just be a matter of testing/trial and error with some configuration parameters on the encoder side.