Did you have them both the HDs partitioned into many segments..? Maybe did you install in the wrong partition..? Have you considered maybe that you might have to reformat and re-partition. I only ask because it sounds like windows isnt recognizing that it was installed on C, or the primary partition...which Win9x requires, also because you said half your HD space is missing... Id try running an Fdisk on it NOT TO REFORMAT, but to see what current partitions are there already. Come back with more info bud, theres plenty of really good help here, many (ok most, hehe) better than mine~!
Rama
" He who (BLEEPS) nuns, will later join the church " Joe Strummer, The Clash - "Death or Glory"