To TS, these are some advices when I have 2nd fresh photographer tagging along:
Communicate with the main photographer, ask him how you can compliments the wedding shots from different angles. Also, try to offer help if you are needed for crowds control.
Remember, don't block him ~ And try to get candids shots assuming the main photographer will take care of the complete events flow.
Regarding which mode to use, learn how to get the right exposure for flash. Once you got it right, you won't need to change it most of the time (thus, use MANUAL mode) under similar lighting and TTL mode for flash.
Hope this helps.