Links between two organizations are defined by a relationship type, similar to links between two contacts. Relationship examples between organizations include customer/supplier, parent company/subsidiary, or 'provides services to'/'is a client of'. Just pick the relationship type and choose the direction (e.g. : which of the two is the supplier and which is the customer) and you're done. Of course you can define additional relationships that might be specific to your type of work under the Settings menu.