To fully utilize your second hard drive for Ubuntu you should use a full install from a live CD/USB rather than a WUBI install. WUBI will put Ubuntu in a virtual partition in a big file inside Windows partition. Even though WUBI is easier as you don't have to partition your hard drive, it has some disadvantages. For example, if the Windows partition gets corrupted, Ubuntu won't boot.
As with full install and WUBI install, you can only use either Ubuntu or Windows at any time. You will be able to choose between Ubuntu and Windows every time you boot the computer. To switch between the two you have to reboot the computer and choose the other OS.
- First download the ISO file then burn it to a CD/DVD or use Unetbootin to get a bootable USB, select the Installation media to boot first from your BIOS.
- Once you're in the Live Session, choose Install Ubuntu.
- When you get to the Choose an Option screen, select Do Something Else.
- Locate the Second drive and choose to Install the System on the second drive.
- Choose to also install the bootloader on the 2nd drive, make sure it's the drive and not a partition (i.e. /dev/sdb and not /dev/sdb1). I am assuming sdb is your second hard drive. It may not be, check to be sure.
- Set the BIOS to boot from the UBUNTU hard drive first, and Windows
- Boot Ubuntu and open a terminal by pressing Ctrl+Alt+T and type
The last step should find the Windows in the first drive and update Grub accordingly and from next boot,you should be able to choose between Ubuntu and Windows.
See How to install ubuntu on a second hard drive with windows being on the first?
I recommend you make
- One 30GB
/ partition format ext4
- One 4GB Swap partition format Linux/Swap
- Rest of the drive as
/home partition format ext4
Ubuntu should be able to use all the RAM irrespective of your choice of 32bit (PAE) or 64bit version. The AMD64 will be more efficient. With 16GB RAM you may not need to swap much. But Ubuntu will be happier with a Swap partition.
Hope this helps