So, if sharing with another operating system make sure to prepare your drive with free space (unallocated) before booting with the install CD.
I installed both ways at different times and it took care of my boot options on install without a hitch. No problems should occur if Windows is the first install. If windows is installed "after" the Pardus install that may create a different issue.
Since it sounds like you may be a new Linux user, I'd just like to add some extra clarification to Freebird's good advice. To prepare your hard drive before you attempt to install Pardus, i.e., to create free space ("partitions") onto which Pardus can be installed, there a couple of user-friendly tools available:http://gparted.sourceforge.net/
GParted Live CD
or, a Puppy Linux Live CD will also have GParted (along with other goodies):http://puppylinux.org/main/How%20to%20download%20Puppy.htm
Basically, what you will do is shrink your existing Windows partition and create two new partitions for your Pardus installation.
I don't know the capacity of your current hard drive, but just to give you an idea / initial suggestion for partition type(s) and sizes, I think this would be a reasonable starting point:
a root partition (labelled as "/") of 10-12 GB in size, with an ext4 file system
(My root partition is 12 GB, but if your space is tight, you can probably get by with a root partition of 2-3 GB).
a home partition (labelled as "/home") for your personal files (Documents, Photos, Downloads, etc.) of 10-20 GB, with an ext4 file system
(My /home partition is 25 GB, but if you need to make it smaller and don't plan on saving a lot of files here, you could create a 2-3 GB partition).
These are only suggestions which are worth about 0.02's each ...
For extra help, please read the Installation Instructions on the Pardus Wiki:http://en.pardus-wiki.org/Installation:Contents
The Installation Instructions for Pardus 2009 are still available. You might want to look at them also, because they are more detailed than the 2011 instructions -- especially with the partitioning steps. If I remember correctly, there have not been major changes made to YALI. http://en.pardus-wiki.org/Pardus:Installation2009