We had a old company with credit card balance of $25000 then we opened a new company on august 2017 with new myob file.

For some reason i made mistake, instead of paying the old card from old bank account and entering in old myob file, i paid it from the new bank account which is for new myob file and new company.

My boss doesnt know this yet because he did not want anything with old company to go in new myob. how do i fix this without raising red flag?

Hi mohinish you simply pay the amount that you paid from new account back to the new account from the old account. If it is a transaction that requires your boss to authorise then i suggest you tell him of the mistake.

Mate, go and tell your boss you made a mistake and then tell him how you are going to fix it:
1: transfer money from old company bank account to new company bank account
2: the deposit from the old company bank account will cancel out the withdrawal from the new company bank account
3: everything is then exactly how it needs to be.

If you attempt to cover this up and your boss finds out you are playing ducks and drakes with the business bank accounts, you will look a LOT sillier than if you stick your hand up and say "oops my bad" as soon as you become aware of the error.

good luck with it, I hope your boss understands that people are human and mistakes do happen
brendan