You request the Form 1100 after lodging the actual visa application. This will give you a TRN and when you then log back on to the SA SS application you click the "what to do next" or "Request Form 1100" can't remember exactly which then it asks you to input your TRN. Your status then changes to Form 1100 requested and sent to DIAC. Due to all the problems people have had with DIAC receiving them tho I am already trying to double check that SA have sent it and that DIAC subsequently receive it. Don't want to leave anything to chance!
Hope that helps?