It wouldn't make much difference really, as you could do the same with both. I have a 120GB drive I partioned into 4 for all the family members, and end up with about 35gig each or something like that (Giving my sister less as all she has is Sims 2 and Cats hehe).
It might be best to have two seperate smaller drives in your case, again if one fails. If you were worried about hardware failure, you could also set the two hard drives as RAID, so that they copy data to each other, but this would make one not possible to use I think...
It depends really on what you want. You'd probably end up with the same amount of space on the two hard drives as you would with partioning a 120GB drive.
My prefrence would be getting two hard drives for a setup like that (especially with the amount of failures I've had). I would say to partiton if you wanted more than 2 setups for saving room in the computer case.
Abit IP35 Pro / Q6600 G0 / Zalman 9700 / 8800GTS 640mb / 4x 2GB Corsair XMS / X-FI Xtreme M / 1x 1TB / Antec 900 / Logitech Z-5500 / Samsung 20inch