Yeah you have installed two partitions by mistake.
One thing you could do is boot up from the drive you want Windows on and then in Windows you could format the other parition to use for data and whatever else, but without re-installing Windows I don't think there is a way to take out that partition unless you use a program like Partition Magic which makes this job easy though does cost you.
How much space is on each partition now then?
1. So after booting on the OS you want, Right click My Computer, and go to Manage.
2. Now, select Disk Management from the list
3. Choose the 2nd partition you want to format to remove Windows from it (it'll still be there, just without windows, and so without the dual boot option, and can have a few good uses)
4. Then right click the drive/partition (probably D) and choose 'Format' from the list. If it is Windows XP choose NTFS to format to, or otherwise choose FAT32. It'll now follow the steps to format the drive.
5. You can now restart, and you won't get the dual boot screen and D will be blank. You will now be able to maybe seperate your games or work files from the main machine just incase Windows goes belly up, and you have to format... this means you won't lose your data if it is on D and you wipe C
Warning: Do not choose 'Delete Logical Drive' from the list. Even though it'd remove the partition, you would not get the Gigabytes of space back on your original partition and so you'd lose space.
Hope this helps