Holy cow, that's a lot to cover. I'll take a turn at some of it.
Yes, you can "ghost" the old drive to the new.
Yes, you can use either drive as Primary or slave.
No, each partition doesn't require an OS - you only need a single OS for the entire computer.
Yes, you ~can~ install Win Me on each hard drive, but there's not much sense in it unless you have a specific reason. If you did that, you would need a third-party boot manager to select which OS to boot every time you started the computer.
I'm not sure about working better with an extended partition, as you read in the article. Having multiple partitions is a good idea, but I don't see why extended/logical partitions would be better than primary partitions - each drive can have up to four primary partitions, or three primary with an extended partition that can contain a large number of logical partitions.
Best Wishes,
Bob