Replaced a bad hard drive.

[Rookie222]

Gateway 700 XL - Windows XP Home - Intel Pent 4 - (2) 512 MB PC3200 RO DDR - (2) 250 GB Hard drives - Maxtor 7Y250MO
This machine worked absolutely great until the main hard drive started to fail. I backed up the entire hard drive and was sent a replacement. No problems. (When I installed the new hard drive -Western Digital - I did not switch any of the connections re: primary/slave - Should I have done this?) The directions given me were very vague. Installed the new hard drive and started reinstalling all the programs. Win XP Home edition failed at the first attempt. Second attempt installed fine. When I now start the computer I am asked which installation do I want to start. How do I get rid of the bogus installation?
Next - It seems as though the computer did its own thing upon installation as all of the drives have changed letters and D: seems to be the primary drive now and it was not before the replacement of the hard drive. The computer works fine. One program out of quite a few installed is acting sluggish. Do I need to start over again?
I took a look in computer management and found this Disk 1 C: Partition NTFS healthy (system) 94% free - Disk 2 D: partition NTFS healthy (boot) 86% free. So I guess I am answering my own question here the computer is booting from the slave drive. The new drive that I installed was supposed to be formatted. Where do I go from here?