RESOURCE.CFG is for the DOS version and RESOURCE.WIN is for the Windows version. I recommend that you run the DOS version of any Sierra game, if available. King’s Quest VI is the only Sierra game that the Windows version has a lot more to offer than the DOS version. The DOS versions are generally more trouble free.
To play SQ6 from the hard drive, copy these files to the installed folder:
RESOURCE.AUD, RESOURCE.SFX, RESOURCE.MAP, RESOURCE.MDT, all of the .SND, .MSG and .SCR files. Also copy the Robots and Movies folders over (you only need the .VMD files in the Movies folder,) too.
just be sure that you edit the config file to change all references to the CD to point to the hard drive instead.