1) Do not be mistaken, I am not an employee for Scoot Airlines. So I am not able to help amend your booking that you have PM-ed me. I am just like another regular TA user here on these forums. I am only able to advise and offer some suggestions.
2) << Flight from Bangkok to Singapore and Singapore to Sydney, so these are on 2 different booking numbers.we want to add Scoot Thru and by email and phone have been told this is not possible.Why can't our flights be changed to one booking number?? >>
Airlines, whether full service or low cost carriers, cannot combine 2 seperate booking booking (or 2 PNR) into 1. They can only do a LINK in the system. To combine 2 into 1, that would be equal to the cancellation of the 2 bookings and re-book as one itinerary.
3) << We were told on the phone we can only get the fly thru at Singapore,not Bangkok..We have no connecting flight from Singapore. >>
Yes, you can get Scoot-Thru from Transfer Lounge E at SIN. I do not understand your comment about no connecting flight. Aren't you doing BKK-SIN and SIN-SYD with a 3-hr transfer window?
4) << On your website it says if purchased from the desk rebooking and fare difference applies if you miss your flight. Does the same apply if purchased at the check in counter?(the website has the asterix for this penalty definately only applying to the desk). >>
Unfortunately, only the airline themselves is able to to give you an answer to this.
5) This airline has a poor record for baggage handling. It would be safer to transfer your checked-in bags by yourself.
6) I would not recommend connecting flights using low cost airlines.