Hi @katie93
There is no need to worry about the ATO's super balance not being the same as in your superfund.
Super funds are not required to report your balance to the ATO frequently, sometimes it is only reported once a year, hence the ATO balance is not always up to date. On your myGov account in the Super tab and then fund details area it should actually list the balance and the date it was last updated.
When transferring your super you are not required to specify an amount on your myGov account. This is because the ATO will send your transfer request directly to the superfund who can view your current account balance and transfer this in full to the new superfund. Hope this helps!