Can I make a suggestion. Since you have Windows on a separate drive, anything you do on the second drive won't do anything to Windows. Therefore, why don't you go through the installation process on the second drive and see how it goes.
At the very worst, you will have to select the OS to boot through the bios (most computers allow you to hit a key to select boot device on startup), but one you have Ubuntu installed, we can talk you through the whole grub thing.
My suggested partitioning setuo would be (assuning 250G drive)
100M for grub (you don't need this, but it can make life easier later)
15GB to allocate to /
1G top allocate to swap (I expect Ubuntu will require a swap partition)
200G to allocate to /home
34G (or thereabouts) left unused for later use.
Note that on most PCs you can only have 4 primary partitions, but more (not sure of the limitations) logical partitions within an extended partition (have I lost you yet?). Therefore, I'd create a an extended partition and create the layout above as logical partitions withing that extended partition.
To be honest, the easiest way to do the partitioning would be to download one of the specialist live CD's like gparted or parted magic. You can get these from www.distrowatch.com
. They have good graphical interfaces that are pretty easy to follow, and I find them better than the partitioning tools supplied with installation disks. You can then just allocate the relevant partitions.
It sounds daunting but it's not that bad, and we'll help you through it. Here are some docs for you to look at
This shows the install process
When you get to the stage that say "Select a Disk", make sure you select your second drive, then the option to manually edit the partition table
Give it a go, and let us know how it progresses.