what operating system ??? xp, 98, 2k
for 98se 32gb primary partition is optimal but ive gone as large as 38 gb's with 98 and i get away with 40-50 gb secondary partitions. with a secondary drive ive had to split 80 gb's and larger into 2 or more partitions .
with xp I myself havent used a hard drive larger then 80gb so i havent found the format / size thresh hold yet ... or if it even has one
now if your just in the setup part of windows and you partitioned that hd then it may be only seeing that primary partition at this time ... WD hard drive can be tempermental when trying to format/partition .. (trick of the trade use a maxtor partition disk ... it works everytime)