I tell you what I did purely for a laugh a while back... Never was sure as to why I did it, and I am still not sure to this day, but...
I customised one of my Windows CDs... I used a Win2K one at the time and my youngest sons PC, I have only one HD in, and so, I set it up to use the following :-
Windows = C:\WinNT\
Program Files = D:\
My Docs = E:\
Temp = F:\
Now, obviously, I gave it 4 Partitions, at the time, I gave it 4GB + 20GB + 10GB + 3GB ( Im sure it was anyway ) and then some time later, I added an 80GB and using Partition Magic, I simply copied D: to the new Drive, Killed off the old D:, gave the new Drive the D: Label instead, stretched C: to 7GB and pulled E: back down, increased that and expanded F: to 10GB and its been like that ever since.
When I first installed it, was when I only had one legal copy of XP, so it must be like 5 or 6 years ago surely...? - Well we are still running that PC ( occasionally anyway ) and as of yet, it has NEVER crashed or anything nasty.... Come to think of it, its never been checked for Viruses or spyware either so I bet once we do, it will find a billion of them and start to crash etc every day.
Anyway, what I am saying there is that in the end its ultimately up to you really.
You need to be aware, that while I feel its better to do things this or that way, and other say do it another way, its all down to you.
No matetr what you do, your data will always be at risk... You use Drive A for Windows and Drive B for data bu there is nothing that says that when Drive A dies, its not going to take Drive B with it? - after all, it might short out, and kill the entire system, so always backup.