dos, you say? You need to either format the first drive as a boot drive (format /s I think) or you can run "sys c:" to transfer the bootableness over first before copying everything else. Really you should be able to do the format before copying files (via a boot floppy).
Geez - this is knowledge circa 1990
edit: link RE format command:
http://www.computerhope.com/formathl.htm