Hi kajostman
When you enable Multi-Inventory for all your products, the first time they are accessed, the Main Inventory gets created for them by copying the actual data from WooCommerce. If you have the manage stock disabled for all your main inventories, I understand is because you had that option disabled on your product before enabling Multi-Inventory, am I right?
I haven't tested it but, perhaps you could disable Multi-Inventory temporarily, go to ATUM Settings >> Tools, and enable the manage stock option for all your products at once by using the tool named "Update WC's manage stock". Once you do so, and you confirm that your products have this option enabled, you can enable Multi-Inventory again and check if the value is updated on your main inventories.
But, please note that when you enable the WC's manage stock option, as you didn't have any stock quantity added for them, all your products' quantities will be set to 0 and become "out of stock". So you will have to enter quantities manually one by one...
An alternative to this, would be using our ATUM Export PRO add-on to export all your inventories and enable the manage stock (and also add the right stock quantities) to the exported file and import it back thereafter.
You can read the documentation regarding this here:
https://stockmanagementlabs.crunch.help/atum-export-import-pro/how-to-bulk-import-multi-inventories
I hope this helps.
Best Regards,
Salva.