SSkim - will not be an issue. Just call the ATO and let them know you are now under PAYG employment.
There could still be some situations where you may have to pay advance tax, but I think you should get the result you want assuming there is nothing else that the ATO are interested in.
I've always found the ATO to be most reasonable and they have issued two private ruling to me this year without too much hassle - both with the result I wanted.
