I deliberately said can be made as oppose to are more... because the technique most people use and which I have witnessed time and time again on the internet is the direct cause of many headaches.
Well no more, I am going to tell you how to create a fool proof dual boot setup featuring 2 disk drives.
The biggest mistake you can make (bad practice)
Most of the problems in a 2 disk dual boot setup are caused by having your Windows disk drive as the Primary disk drive on your system and the intended Linux drive as the Secondary drive on the system.
With this disk setup, when attempting to install a Linux distribution it will always default to automatically suggesting to install or installing the Grub bootloader to your Primary Windows disk drive.
It is important to note that the reason why Grub wants to install on your Windows drive is because it is the Primary drive on the system.
Assuming you proceed with such a setup the end result is potentially for the majority of users a bad result.
Why is installing Grub on the Primary Windows drive in a 2 disk dual boot setup bad?
/dev/sda ---- > Windows --- > Primary Disk ---- > Bootloader (Grub boot files on /dev/sdb)
/dev/sdb ---- > Linux ---- > Secondary Disk ---- > No Bootloader
If you were to disconnect your Secondary drive or it fails, your Windows operating system will be unbootable because the Secondary drive contained files required by the Grub bootloader to boot the system.
In the opposite situation, if you disconnect the Primary drive or it fails, the Linux operating system will be unbootable because no bootloader is present.
Therefore the biggest disadvantage with this setup is the system is dependant on the presence of both drives. Should either of the drives cease to be present or function you cannot boot into Windows or Linux.
Most Linux distributions do allow you to change the default grub installation settings, and if you plan to keep your Windows drive as the Primary drive on the system make sure you install grub to the Linux drive, /dev/sdb.
It is far more advantageous to have each drive independent from one an other and capable of booting on its own.
But there is a better more fool proof way!
If you want to ensure avoidance of the possible problems the above setup can cause there is a very simple solution. Physically make your Windows drive the Secondary drive on the system and your intended Linux drive the Primary.
By doing this, distributions such as Ubuntu, Fedora, openSUSE will always default to installing the bootloader (Grub/Grub2) on your Primary and intended Linux drive. You can therefore blindly install a distribution and your Windows drive will remain untouched.
SATA port 1 > SATA port 2
If you have two SATA hard disk drives, connect your intended Linux drive to SATA port 1 and your Windows drive to SATA port 2. This will permanently make your intended Linux drive the Primary disk drive in the system.
If you are still on IDE drives, remember that the Master end of the cable is the Primary, and that IDE channel 1 takes priorty over IDE channel 2.
Additional guidance for Ubuntu 11.04 users
During the installation choose the "Something else" option and create your partitions manually.
Ubuntu 11.04 - Creating a 2 disk dual boot setup
In the above screenshot, I have placed my intended Linux drive in SATA port 1 and my Windows 7 drive in SATA port 2.
The Ubuntu installer has identified my intended Linux drive as the Primary drive on the system (/dev/sda) and has by default suggested installing the boot loader to /dev/sda.
My Windows 7 drive therefore by default remains untouched.
So if you are the forgetful type or want to ensure no mistakes, making your intended Linux drive the Primary drive on the system will help.
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