Two options: manually partition, or run the risk of windows being wiped. Not really sure what it will do in the case of auto partition.
For a manual partition scheme, make sure that your / partition is either /dev/hda1, /dev/hda2, or /dev/hda3. These are your primary partitions, and Linux may or may not play nicely if it's on an extended partition.
My current partition scheme:
/dev/hda1 - Win2k - 15 gigs
/dev/hda2 - Linux - "/" mountpoint - 35 gigs
/dev/hda4 - Extended partition - 10 gigs - Consists of:
/dev/hda5 - 100 megs - Linux "/boot" mountpoint
/dev/hda6 - 900 megs - Linux swap
/dev/hda7 - 9 gigs - FAT32 - Media & storage for both OSes
Now what's vital out of this is the following:
"/" mounted on /dev/hda1, 2, or 3
"/boot" a decent size (some recommend 32 megs, others recommend around 100 megs. Something in this range should be fine).
Your swap space should be placed on another partition and should be at least double your amount of RAM, more if possible (I have 312 megs of RAM and 900 megs of swap, and things are pretty smooth).
That should give you a real nice partition scheme. Add whatever else you want (some like to make "/home" separate, but it's not needed and I quite frankly don't like that). If you're dual booting, I'd also recommend a media partition (FAT32 file system) for things like storage, passing files from Lin to Win, and general miscellaneous use. Makes life a lot easier when both OSes can see the same space.