You should be fine, and might just have to adjust the boot order in the BIOS to make sure that your current drive is set to be the boot drive.
That said, I would suggest running a test on the new hard drive before using it as storage space. If it is loaded with bad sectors then you are just looking to get lost data. Even just checking the SMART data on the drive would be a good idea, but I'd suggest something that scanned the whole thing.
Once you have the drive in place and are booted back to PCLOS, you can use gparted or the KDE partition manager to format the drive to something usable. For storage, you could format it to EXT3 or EXT4, or NTFS. It will be a separate drive, so you would need to move things over from your main drive if you wanted to free up space on it. Music, video, and large downloads could all go on the secondary drive, keeping your main drive from getting bogged down.