Safely Disabling a Hard dirve

With PC Off, remove power connector and IDE cable connector if it is on same channel with other drive.

That should be all that's necessary.

If not an IDE or SATA drive, post back with more info.

If Windows is set to run a page file on the drive, it would be wise to remove the drive from device manager before shutting down and disconnecting the drive.

If you unplug the drive, you need to verify that the jumpers on your other drive are set correctly.
For many hard drives, the jumper settings are different for Master with slave present, and for single drive.

You can also "soft" disable the second drive by setting the drive type for that drive in BIOS settings to none.

I am curious to know what kind of problems you are having since adding the second drive.

I have a few pointers for you:

While most manufactures will tell you otherwise, I NEVER set up a dual drive system with 2 different manufactures hard drives on the same IDE cable.
Some drives just don't play well with other makes of drives.

Was the new drive too large for your BIOS to detect it properly?
If so, did you install the drive overlay software that came with the hard drive?
These programs can cause a variety of system problems.
If a new hard drive is too large for your BIOS to recognize it, I recommend installing a PCI IDE controller card.

Have you moved programs or just data files to the new drive?
For nearly ALL programs, it is "best" practice to un-install and then re-install the program on the new drive.

How large of a power supply do you have?
Depending on what other hardware has been added to your system, you may need a larger power supply.

Chas

The problem i am troubleshooting is my pc will freeze up several times a day. I thought it was my cd drive at first, since usually when this happens the cd drive will spin up right before it locks up. I removed the cd drive but still same problem. It seemed to all start when i added a 2nd 40gig Western Digital drive. First had it as "choice select" thought maybe that was the issue, changed it to a master slave.

Still the same problem, i have a hunch its an issue with the ide controller, have updated all bios and ide drivers. Both drives are Western Digital Drives a 20 gig main and this 40 gig slave.

I'd like to try and remove the 40gig, just to see if my hunch is right or not. Good point on the page file, i will have to move that back to 20 gig drive if its not there already.

This has expanded from original question which was thoroughly answered. Next time ask what you intend at first.

I would change power supply before doing anything else.