You really should use both external FW800 drives if you have two. Premiere loves sharing the load onto more than one drive. For example, put media, projects, and scratch on one drive and put media cache, media cache db, and outputs on the second.
Regarding the real world performance difference, you should check all the cache settings in Windows for how both drives are configured.
Thanks Jim, indeed I am using 2 firewire 800 drives. Are you then saying that media should be on the same drive as the project and cache? It did seem faster rendering when everything on the same drive and after moving the media to the faster drive it was actually slower at rendering. This kinda goea against what Adobe reccomends.
One question regarding your IEEE-1394b (FW-800) connections: does your connector have separate controller chips for each connection, or does it have one chip for multiple connectors, or are you perhaps daisy-chaining the drives?