Which distro did you use? If you used Fedora or CentOS, they often partition the drives with logical volume management for some reason. You probably need to boot off of a live CD (preferably the rescue disk for your distribution). Before doing so, put both drives back into the Linux system installed the same way (i.e. plugged into the same ATA or SATA channels, with the correct master/slave setting if using regular ATA). If you do have things partitioned with LVM, hopefully they will be mounted automatically so you can copy your data off. If your partitions aren't mounted automatically, I suggest doing fdisk -l to see what partitions are available on your disk. Please post the results here if you do not know how to try and manually mount the partitions.
Whatever you do don't do something unless you fully understand the consequences. That is the surest way to run int otrouble. If possible, I'd suggest dd'ing both hard drives onto back-up media before proceeding further, in case you really do manage to mess something up.