Jaime, the A/P Invoice Batch is the only Batch Type Import which allows you to map the Company at the Invoice/Header level.

In order to map the OrgId/System Company you would need to have a three level hierarchy: Batch, Header, Detail; the Batch level specifies the System Connector.

To achieve this you will need to add a hierarchy transform into your existing integration. I recommend creating a brand new branch of processing, and once you're happy with the results delete the old one.

Below is a set of screenshots which describe how to do this.

0 - Design Setup with corresponding numbers for the screenshots.

1. The existing two level hierarchy.
2. Add a new Hierarchy transform, click the Field Mapping, then press the Edit button.
3. Deselect all the fields to remove the invoice related fields, leaving on the batch related fields. Specify the OrgiD field as the only key.
4. Create a new transaction (Invoice), set the parent property to the top most transaction, and the Copy Child transactions to the newly created transaction (Invoice). Press the Edit button.
5. Setup the Fields on the new Header transaction and set the Keys accordingly.
6. Press Refresh...you should now have the data grouped by OrgId/System Connector Id.
7. Add the Sage300 Connector, click the Field Mapping. Associate the top most transaction to Invoice Batches. You will see the System Connector field.
8. The newly created transaction (Invoice) will be sorted to the bottom, despite it logically sorting to the middle transaction.
9. Select it, and map it to the Invoices level.

I hope this describes the steps.