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When you use MYOB's super portal (available late June) to pay superannuation, the money will be automatically paid from your bank account. But this won't affect your MYOB Essentials accounts. You'll need to record the payment transaction yourself.
If you've got bank feeds on this bank account, this is easy. When the super payment transaction appears in your bank feed, just allocate it to your Superannuation expense account.
If you don't have bank feeds, you can create a Spend Money transaction for the amount of the super payment. Allocate it to your Superannuation expense account.
For more information about paying super through MYOB's super portal, see Pay superannuation.