Superannuation hasn't gone to employee funds

Hi,

I have just realised that the super hasn't been going into the employee funds for about 8 mths. I have been learning MYOB on the run, I have been paying the Super each quarter to the ATO, as I was told but I wasn't aware that I had to pay it into the employee funds. I thought the ATO did that, yes I know probably naive of me, but like I said I've been learning this on the run. How do I correct this without paying the ATO again?