There are many approaches to doing this for protecting your server though personally the worse thing is to have none when you need one. We have put together a really simple down and dirty approach to backing up IIS 6.0 meta backup below. This approach first creates the backup then renames them to the current date. We run the first bat file daily to assure your system is protected.

@ C:
@cd %systemroot%\system32

@cscript iisback.vbs /backup /b backup

@cd %systemroot%\system32\inetsrv\MetaBack"

ren backup.MD0 %DATE:~4,2%-%DATE:~7,2%-%DATE:~10,4%-backup.MD0
ren backup.SC0 %DATE:~4,2%-%DATE:~7,2%-%DATE:~10,4%-backup.SC0

Then to avoid the folder from filling up and retaining 7 days of backups we just run a second script we only run once a week.

echo on
rem Delete Meta Backup File
FORFILES /p C:\Windows\system32\inetsrv\MetaBack /s /m *.MDO /d -7 /c "CMD /C del /Q @FILE"
FORFILES /p C:\Windows\system32\inetsrv\MetaBack /s /m *.SCO /d -7 /c "CMD /C del /Q @FILE"
rem