ok check this.
Buy partition magic. Install it.
Resize your partition for windows to small, just a couple gigs more than the total size.
Make a fat 32 partition for data in which you need for both.
Make a linux ext3 and linux swap partitions.
Do the install and install tothe ext3 and do not use the st00pid druid
But wait wait wait wait wait.
You say you have two partitions and both are ntfs but one is empty and you wish to make it ext3?
Are you SURE its empty and a second partition, AKA NOT a part of windows?
In that case, go to the manual partitioning things with the druid and DELETE the second partition.
And if it is just one partition, still use the manual partitioner, but use the 'Edit' part to change the size of the ntfs partition.
Then make the linux ext3 (label it as /) and then make a linux swap (no label needed). The swap should be around 2x your ram.
I do not think the auto-druid will resize your ntfs partitions for you.