It is okay to have Windows loaded on both
hard drives. it won't go berserk over that.
When you have to HD connected, naturally one
will be treated as a boot disk and another just a D:\ drive. In this case, your master drive will
be seen first. That will make the slave just a
secondary and will not be booted from. So, generally speaking, it will boot from one and
treat the other as just a storage (One is a C:\
and the other a D:\, in that order. You should
remember and know which one is which, though because the letter assignment is automatic, the one booted from is a C:, etc.
This confusion is multiplied when you have
partitioned you HD into several logical drives.
I have an example to show about this which
caused me the good orginal C: (boot) drive.
I used Win ME and I had two physical drives
connected just like you are doing. My original
20 Gig was partitioned into C: and D: drive. The new drive I bought to put in is partitioned
as a C, D, E (three drives when connected alone). When I connected both of them to the computer, I thought the original two would stay C and D and the new one would become
D, E and F respectively. Well, they did, only with a cross-over of a D become and E and the partition that should have become the E part of the new drive became D of the mix.
When I did a format of the new drive (connected together with it set as master) the machine inadvertently took out the C part on the original which was the boot drive.
The best way to do it without confusion is to disconnect the other when you work on one. You can work on one unit until you have it just the way you want then connect both of them
using the master/slave relationship. One good
thing about having both drive bootable is that
on some motherboard (not sure if new generations allow this anymore but I used to have one that alloed me) you can set to have it boot from either Master or Slave. So with this you won't need a boot manager.
The answer to you last question is when you have both drives connected you can copy files or folders from one to the other as you normally would be able to. This includes the Windows folder(with some components excluded) as well.