Your 120GB HDD is newer than your 20GB correct? Use the better drive as HDD#0. You want Windows working on the best drive.
Here's my "official" HDD/Part. recommendation
PP=Primary Partition:EP=Extended Partition
HDD#0=120GB HDD / HDD#1=20GB HDD
HDD#0:PP/"C" 30GB (Windows)
HDD#0:EP/"E" 30GB (Flight/Games)
HDD#0:EP/"F" 90GB (Application Storage)
HDD#1:PP/"D" 20GB (Programs)
Here's why:
C: By placing Windows on the primary partition it's closer to the front of the disk for faster reading.
D: Place Programs here: First I need to explain how I think. I consider "applications" to be any program which produces a "user file" (Word, Excel, Paint etc.) Utilities are programs which do not (Anti-Virus, Spyware etc)
Do not install anything to Program Files. Also, place your SWAP file here.
E: Placing the Flight/Games on the first Extended Part. Keeps it on the best drive, as close to the front as possible.
F: Anything you have created. Word docs, images (drawn or captured), aircraft (created/downloaded...) You get the idea?
ADDITIONAL: Set your SWAP file size to be 1.5 times the amount of RAM. I have 1GB Ram, Swap file is 1534MB.