Ditto on the green rails. In addition, if you didn't order a (useless) floppy drive with the computer, you'll be able to squeeze the additional HD into the floppy slot, which gives you some more separation from both the other hard drive as well as your optical drives, hopefully giving better airflow and cooling.
A bigger problem is not where to mount your drive, but whether you've got anything to connect it to. There's only ONE p-ata port on my Dell 8400, and I think that's the case with many current dell models. This means if you've got two optical drives, or one hd and one optical, you've got no more connectors left for the other hard drive. I'm assuming your 40gb hd is p-ata, since I've not seen any s-ata drives that small. If it's s-ata, of course, then you've got no problem, since there's probably going to be 4 s-ata ports on the mobo.