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:
http://autodesk.blogs.com/between_the_lines/2003/09/merge_multiple_.html
Another alternative would be to use the Sean Dotson AutoSave DWF utility which simply publishes a DWF every time you save:
http://www.mcadforums.com/forums/viewtopic.php?t=2076
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