I see you're still at it, nicola. You're going to ask the OP to build anew computer? And you're asking him to skip 9 years of security updates? And Panda is free, BTW.
I don't know about speed, but you can put Windows and the program files on either one, strictly from the OS point of view. However, Windows +Program files might be only 10 or 15 GB, and your data would be far more, so it's not rational to put them on a 250 HD. My Windows with all updates +96 programs and utilities, takes up only 6.5 GB.
The HD with the OS must be designated active. Since they're on separate channels, they will both be master on their own channel. However if you have a CD-RW or DVD-RW on the IDE channel, it doesn't matter whether the Data HD is master or slave. It matters only with an OS drive.
After installing the OS, download SP3, which also contains SP2, then all the updates since SP3.