When sending outbound documents to a VAN, you should configure the VAN as a trading partner using the Gateway protocol.  All trading partners sending documents via the VAN must set the "Use Transporting Gateway" setting to the VAN trading partner.

By default, BC will generate batches with multiple ISA-IEA or UNA-UNZ segments in one batch to the trading partner depending on the batch frequency or transaction count.  Some VAN require batches to be done on a trading partner by trading partner basis, with only one ISA-IEA or UNA-UNZ per batch.  To accomplish this, go the the VAN trading partner Gateway properties>Batching tab> Always Create Batch per Trading Partner and check the box. BC will then generate batches on a trading partner basis