STP - Nonsuper Salary Sacrifice

Hi. I've browsed the community extensively & I now know what I should have done to meet the requirements of STP reporting. Unfortunately, when I started my job 12 months ago, nonsuper salary sacrifice (we are a not for profit charity) was setup under Superannuation instead of deductions. I was told that it was set up this way because it was the only way they could get the tax calculating on the correct gross wage. I had no experience with MYOB prior to this position so I was none the wiser. My research of this community has discovered that the correct way to set it up is to create the salary sacrifice amount as a Deduction then Exempt it from tax. All of the employee data to be finalised for STP, shows the gross wage prior to the salary sacrifice amounts which is incorrect. We elected to introduce STP early (March 2019) due to less than 19 employees. I'm thinking at this late stage it's best to phone the ATO to see if I can submit payment summaries as normal for 2019FY & change all of the salary sacrifice deductions in MYOB for the new FY. Can anyone please advise if my thinking is correct? I plan to phone the ATO tomorrow. Thank you!!