I need a little more information to know what is going on.
With what you tell me, my suspicion is that you are not activating the ATUM control on the products you already had created.
Go to the WooCommerce product list and open a product that does not appear in Stock Central, look in the ATUM inventory tab to see that the ATUM Control Switch option is enabled. If it is not, activate it and you will see that it already appears in central stock.
If finally it was this and you don't want to go one by one activating the control, you can go to ATUM->Settings-> Tools: and you will find this tool that allows you to do it in bulk.