hi,
the best way is partition your disk as how much you need for your windows OS & install windows, leave the remaining unportitioned. install Linux. it will use the unportitioned space for linux installation. The important issues are You can have a maximum of 4 primary partitions. so have one primary dos, one for Linux native and others as you like. for better performance have a separate boot partion.
Make sure that you install LILO boot. it is used to select your desired OS at the time of booting.
if you need further help mail to me at simp_raman@rediffmail.com