You don't have to have to have Linux on a separate partition, which distros such as SUSE7.1 LIVE and Mandrake can also be installed on a windoze partition, but you wont find that it is as good as giving Linux its own partition.
To give Linux its own partitions, you need to make some empty space on the HD, and you may be able to delete the partitions which windoze cant find (is this the prob?).
If you have both Linux and Windoze installed then you will have a dual boot system which means you will have to install either LILO or GRUB to your MBR (Master Boot Record), which will allow to boot either Windoze or Linux, or anything else for that matter!
. This is done during the install process, so you don't need to worry too much about it. However, it will stop you from booting any operating system on the comp if LILO or GRUB are not set up correctly.