Hi Sara,
The intercompany process starts from Purchasing. IF you have two companies in the same ByD system and want to exchange goods between them, the buying company will have to raise a purchase order to the selling company via a purchase order. This purchase order will automatically become a sales order for your seller company while the buying company will be the account for the sales order.
This is why you need to configure/select only purchasing related question for intercompany process. If you create a direct sales order, you will face issues when you create customer invoice against the intercompany sales order. The system will try and create an automatic supplier invoice and this invoice document will not be able to identify a purchase order or a delivery document for it to be posted against.
You can refer the help document titled "Intercompany Stock Transfer" which will explain the above scenario in detail.
I hope this helps.
Regards
Anand