The first OS to install on the new drive is Windows followed by the root and swap partitions needed for ubuntu. Any Windows installation requires the mbr on the first part of the drive. You may prefer to use the old drive after retrieving your files from onto the new Windows drive for running Linux there. This is another option coming from someone who has dual OSed more then once.
To partition the new drive only you would need to perform a custom installation of Windows by reducing the size of the partition to create once you have the installation phase. The installer will detect both drives if they installed at the same time. So you may want to unplug the second drive to avoid any accidental deletion there. Once drive #1 is seen as the drive listed look at the total drive space available. You can easily lower the entire drive space down to the amount of space you want for Windows. Linux doesn't require a large amount of drive space like MS does. Anywhere from 150-180gb would be good for the Windows primary partition.
Following the installation of Windows you will need a partitioning tool for Linux in order to create the root and swap partitions. A good 3-5gb is plenty for the swap while the second partition after Windows should be the larger root partition where the Linux files are unpacked to. Once partitioning tool that will create the partitions for both Windows and Linux is the GParted(Gnome Partition Editor) found at
http://prdownloads.sourceforge.net/g...1.iso?download
Once the partitions are created the Windows installer will format the first partition for Windows to go on and the Linux version of fdisk or cfdisk is used to format the two for ubuntu. GPart is a free program that will need to be burned to a cd and made bootable. The free version of BurnOn which has worked quite well here can be found at
http://www.burnworld.com/burnoncddvd/