VS2008 IIS7.5 Server2008r2 FTP and virtual directories

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IIS7

VS2008

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Visual-Studio

FTP

I'm trying to migrate to new boxes running MS2008r2 IIS7.5 on a network using Visual Studio 2008. I'd like to use ftp rather than file folders so that I can ftp from home, etc. Bloth the development site and the production site are located on the MS2008r2 server with backups every night. When I ftp to the development site, the virtual directories I've added to the root web appear. When I try to publish via ftp, the webconfigs in the virtual directories cause errors. When I load and publish via file folders, I don't see the virtual directories, everything is published fine. I'm new to IIS7.5 Is there a way to ignore child virtual directories when publishing via ftp?

Thanks,
Janet