It will be fine.
What is the capacity of the 2nd hard disk, and how much is remaining un-used?
I would recommend you do your partition editing within Windows where your going to be most comfortable.
To do that, click start, and then type in the text box Disk Management and hit enter. It will then open up your physical drives. If your 2nd hard disk is one physical partition, select the partition and then right click the mouse, and select "Shrink Partition" Set the amount to shrink the partition, hit OK, and then leave it to re-size, not using the computer until its done.
Once its resized, select the black unallocated disk space you've just created, and right click and select "New simple partition", fill the boxes in and then click ok and it'll make it. At this point, note down the exact size of the partition (this will be your confirmation in Linux that you have the right disk).
Then reboot and run the installer. I highly recommend the step by step guide in my signature below this post. It will explain in detail all the steps needed, and will also aid you with the advanced partitioner, as this is going to be best to ensure you use the correct physical disk.
Once your in the Linux partitioner you can delete the new simple partition you made, and then use the free space to make your / (root) and SWAP partitions.
Some Important points!
1. Do not assume that the first disk in linux is your first hard disk (e.g. C
in Windows.
2. Letters for drive names are not used in Linux. It will be refered to as sd (SATA Disk) a (the first, b is second, c third etc) 1 (partition number) = sda1
3. Linux requires at least a / partition to function. If you plan to keep using it long term I suggest you also alocate a /usr and /home partition, and SWAP space (the size of your RAM min of 2GB is fine - I have 4GB RAM 7,5GB SWAP which really isn't neccessary).
4. Install the bootloader to the hard disk with your Windows 7 on it. (not a partition, but the whole disk. It will do the rest for you.)
