create your new folder locations (this can be done by copying the current inetpub folder to a different drive/partition) or manually creating the necessary folders
to move the websites use IIS Manager (right-click on each website, and update the root of each website). You can do this programmatically by using adsutil.vbs
do the same for the FTP sites
to move the SMTP service's folders, use the following script: (watch for wrapping!), they are
"cscript.exe [directory]/[file.vbs] set smtpsvc/1/[command] [dir destination] cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/dropdirectory E:\Repository\Inetpub\mailroot\drop cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/badmaildirectory E:\Repository\Inetpub\mailroot\badmail cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/pickupdirectory E:\Repository\Inetpub\mailroot\pickup cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/queuedirectory E:\Repository\Inetpub\mailroot\queue
Change x:\mailroot to be the place you want the other folders to go into.