Lex - when you boot up to the LiveCD and get to the partitioning screen, you're going to see all of your partitions listed. It'll be obvious which belong to windows seeing as though they will be tagged as NTFS.
Like, for me, I set up Ubuntu in a different way.
I use 1gb swap, 15gb root ( / ), and the remainder of my hard drive home ( ~ ).
So when I want to reinstall the operating system only, I format the 15gb drive and mount it to root ( / ). Then I install the OS on that partition and all other partitions are left untouched. Just make sure all other partitions do not have a check box in the "format" column.
You don't have to worry about the dual boot issue at hand. You can install Ubuntu overtop of the old Ubuntu 300 times. Grub will still work fine. It's only when things work in a reverse order (XP having to be reinstalled) that you may run into some Grub errors.