What I would like is to have Ubuntu installed on my 60GB SSD and Windows 7 installed on my 1TB HDD in a 100GB partition, leaving the remaining 900GB as a NTFS data partition that I could access from Ubuntu or Windows.
My PC boots in UEFI mode, which seems to throw a wrench in most of the currently available guides for setting up a dual boot situation with Windows and Ubuntu.
My first attempt at this was to install Windows first. I pointed the installation at the second hard drive and let it go. Everything went fine, and I could boot into Windows just like you would expect. When I booted into the Ubuntu live CD, Windows was detected, and I chose the option where you can look at the current partitions and set them up how you would like for the Ubuntu installation. I discovered here that Windows had put a 100MB partition on the SSD, which is the "system reserved" boot partition, and the actual Windows OS on the HDD. I was hopeful that the Ubuntu installer would be smart enough to deal with this, and went ahead and installed Ubuntu the SSD. The installation completed successfully, but I couldn't boot into Ubuntu, no matter what options I played with in the boot settings.
I tried this process again, this time disconnecting the SSD before booting the Windows installation DVD. This left the SSD untouched, but I still couldn't boot into Ubuntu after a clean installation to it.
Having Ubuntu running properly is my first priority, so I opted to get it installed and running first, which is where I am now.
The 60GB SSD currently holds a booting, working Ubuntu 12.04 installation. In GParted, it is /dev/sda, and its partitions look like this:
Partition File System Mount Point Size /dev/sda1 fat32 /boot/efi 100MB /dev/sda2 ext4 / 48GB /dev/sda3 linux-swap 8GB
I haven't really touched the 1TB HDD (/dev/sdb), so it looks like this:
Partition File System Size /dev/sdb1 ntfs 932GB
My concern is if I now try to install Windows to the HDD, will it overwrite something on the SSD which will orphan my Ubuntu installation? If so, is that something that boot-repair or some other tool/process can resolve?
If I disconnect the SSD and install Windows to the HDD, will the SSD still be recognized as a bootable device when I reconnect it? I really don't understand how UEFI works, and I don't know if disconnecting and reconnecting drives is safe.
What is the safest way to proceed given my current setup?
Update: rschuler provided a couple of good options, but I would like to be confident that I am not going to lose my current Ubuntu installation when I install Windows. I'm putting up a bounty to see what else is out there.