OK, so here's a quick sequence as a guide:
Format SD card as NTFS: How to Reformat an SD Card Into NTFS | eHow.com
Create VHD to fill it: Create and Use a Virtual Hard Disk on Windows 7
Mount and create folders in VHD (Documents, Music, etc) and Add them to Library : Include folders in a library
Create script(s) to mount VHD at startup: Windows 7: Auto-Mount VHDs at Startup « martin w. angler
While creating the scheduled task (or edit it afterwards) make sure Execute only on AC Power is ticked OFF.
Those not familiar with accessing system functions in RT desktop, "Win+X" is your friend.
Then make sure the new Documents, Music, etc are being indexed by going into "Indexing Options" in Control Panel. When you mounted the VHD and added the folders to the library, those folders should have been added automatically to the Indexed Locations.
Now, reboot the Surface. First, check the VHD mounted automatically (i.e. you see the drive you assigned to the VHD in Explorer). Second, go back into Indexing Options and make sure the folders are still there. This means that they'll continue to be indexed correctly.
To get content on your Surface here on in, it may be easier to use Homegroups or activate the SERVER service in services.msc and share those folders on the VHD. You can Google more on those.