No, entirely up to you how you arrange them. Many people start off with just one drive then buy a larger drive at a later date. This will explain why the O/S is on the smaller of the two drives, but of course there will be other reasons as well.
If I was to reformat a system with two drives, I think I would separate the smaller drive into two partitions, anything upto 10Gb for the operating system and drivers required for hardware then a similar or slightly larger partition for all the applications such as Office etc.
Second or slave drive would be in two or three partitions, first one for a backup of everything on the C: drive then two partitions for all my data.
There are no hard and fast rules for this and many members will have their own preference, some with the opinion that with modern machines and operating systems there is no need to partition a large drive and in fact better not to. You can also mix drives of different speeds on the same IDE channel and the IDE controller will let each drive run at its respective speed.
So, some people will have their master hard drive and one optical drive on one channel then their second or slave drive on the other channel with another optical drive.