Remember that your BizTalk server is simply the mechanism that creates and tracks BizTalk documents. The BizTalk server's job is not to replace all the back-end processing that your company currently does. The BizTalk server you choose should have a multifaceted interface that allows you to send information to and get information from your BizTalk server.
The API should have the kind of hooks you need to communicate with back-end processes, including order fulfillment, accounting, production workflow, customer tracking, sales, and the hundred other systems that might require an interaction with your business partners.