Hello Mathilda
First, can I confirm if the company was using STP through Quickbooks for those first five weeks? If so, this would mean that the company is already registered under one Business Management Software Identifier (BMSID) with the ATO, and when you start STP through MYOB, the company will have a second BMSID. This is fine, because at the end of the year the ATO will combine the data from all BMSIDs for the same business. But, the key in getting things set up with MYOB would be to avoid having duplicated information under two BMSIDs.
I apologise if you already knew the above, but it is worth mentioning just in case you weren't aware. You did mention you have entered the 5 weeks of pays into MYOB but I just wanted to ensure that those 5 weeks have been voided in the old software and reported to the ATO, to avoid any duplications at the end of the year.
As for that first pay you have done in MYOB without setting up STP yet, now that you do have STP set up in MYOB, it will recognise to pull all previous pay data through for YTD totals when you process your first STP pay. That first pay will get reported with your next payrun. If you don't want to wait until the next pay for this to happen or you want to just check that everything will update, you can process a $0 pay (follow the steps outlined here for AccountRight) which will act as a forced update. The employee YTD totals should update accordingly. A few articles which may be useful for setting up MYOB with prior data: Importing data, Enter historical information, and Setting up STP.