Your best bet would be to fdisk, format, and SYS the drive from inside MESS using a boot disk of the appropriate DOS version, and then copy over your data files afterwards. If you just copy msdos.sys etc. it won't work because they won't go into the right sectors.

Personally I don't use imgtool/wimgtool for working with CHD files because it's pretty buggy, I copy files a few at a time to floppy images created with WinImage and then copy them inside the emulation. This would be kind of a pain for a whole hard drive's worth of files though.

The PC hard drive code also has some issues at the moment so I'm not sure if everything would work even if you did it all exactly right.