The first thing you should do is install Windows: During the installation, use the Windows CD to create a partition for windows and leave some unpartitioned / free space for Linux.
For example, on a 500GB HD, you could use 100 GB for a first windows partition and leave 400G of unpartitioned space.
According to what you said about your mother board, using the Windows CD to partition will automatically create an MBR partition.
After Windows is installed and working, boot with the Ubuntu CD and use GParted to create the necessary partition to receive Ubuntu.
Ubuntu (like Debian), can be installed in both kinds of partitioning systems, GPT and MBR. So no problem, just use GParted to add another partition. But pay attention not to touch the already created first partition (the one you created during the Windows install).
For example you could create an second partition type ext3 of 100G for your Ubuntu install, (there should remain 300GB of unpartitioned space on the disk).
And go on with the Ubuntu install. If you do everything correctly you will end with a dual boot HD install (Windows/Ubuntu). Good luck!