Autodesk Vault will automatically publish a DWF each time an IDW is updated. To get auto-publish DWF with Autodesk Vault 4, you manually attach a DWF to the IDW and then specify a publish folder to which the "attached" DWF will "update itself to" upon a check-in. There is no way to "automatically" combine DWF files from multiple IDWs; however, this can be done manually with Autodesk Design Review (formerly known as Autodesk DWF Composer).
Alternatively, you could consider a merge DWF utility available at:
Another alternative would be to use the Sean Dotson AutoSave DWF utility which simply publishes a DWF every time you save: