i've said this a fair few times before, but i've 8 minutes till the program i want to watch starts so i may as well say it again.
personally *I* recommend keeping windows and linux on seperate drives where possible.
As they are seperate you (should) start off with the piece of mind that they are physcially seperate and so you shouldn't need to worry as much with partition worries and similar. you can even disconnect the windows drive and put it on the desk while you install linux... not exactly likely to overwrite windows that way is it?
also as tehy are seperate it makes booting them conceptually much easier and more straight forward (although you will need to fiddle a *tiny* bit to get windows to work properly.) With linux on a master drive and windows on a slave drive you *NEVER* need to touch the windows drive to have a full dual boot system. with linux as master all that you need to do to remove linux from the system is to swap the drives back over and you'd never know...
There's not really any ACTUAL benefits or drawbacks on either system AFAIK, but it's much easier to understand. When you are used to linux and are more confident you'll be pretty indifferent when you are used to messing with individual partitions