I have a similar situation going. I left windows running my array. LinuxMCE can use Windows file shares.
Linux can read NTFS but not write to it reliably.
If your "server" is the only machine that's up 24/7 you can run LinuxMCE core under vmware on the server so it can still perform LinuxMCE server functions. Just don't count on doing multimedia video on the core under VMWare.
Thanks, but that sounds a bit complicated. I think I may just wait until I can build a dedicated Core and have it read the windows shares from the server. One question though. You said linux doesnt write to NTFS reliably, so would it not be a good idea to have it rip movies or record TV to the windows server?