OK, I see now what you are saying. I will retract my comments - sorry.
I agree that placing two hard drives so they are physically touching one another is not desireable, from a heat standpoint if nothing else. However that being said I'll also add that I have seen many PCs where the hard drives were placed together simply because the cases where packed completely full - one of my PCs at home qualifies for this. It is usually not a problem, but a better solution would be to just buy a bigger case.
From a statistics stand point, I used to run a service desk at a computer retailer, moved on to do Helpdesk/PC support for a telecom company. I figure I've been inside several thousand PCs by now (most amusing was a customers PC that had sucked in so much cat hair that it caught fire and melted the motherboard).
Blip, the answers to your questions might vary a bit depending on what OS you are using, but generally speaking:
1) If a drive contains merely data and nothing else, any form of file copy will work. I usually keep a few Win98 boot floppies arround and keep Xcopy on them for this purpose.
If however your OS is on the drive, it gets a bit more complicated. Many copy utilities will not touch a windows registry or other hidden files. I HIGHLY recomend getting a utility like Symantec Ghost or Powerquest Drive Image. Having one of these makes cloneing a drive very, very easy. They are also great for making drive or partition backups, and if you have 2 drives in a system they are even more useful. You can copy an image of your system drive, write it out in 650 meg chunks to your data drive, and then move them to CDR. Then if your system drive ever dies, you replace it, boot up from a floppy with a CD driver, and you are totally restored in minutes. When you support hundreds of PCs like I do it's a real time and life saver.
2) Yes jumpers need to be changed. Each IDE controller can handle two devices, a master and a slave. On some drives (Maxtor) the setting for Master is also used for single drive. on others (Western Digital) there are seperate setting for single drive, master, or slave. These setting are nearly always written on the drive label, so the time to change them is when you have the drive out of the system, before mounting it.
3) Partitioning is something that has to be done regardless of whether a drive is the boot drive or not. Even if you want the drive as one big space, that is still a partition. If you are using the FAT32 file system, I usually use a Win98 boot floppy and just run the old FDISK utility. If the Primary IDE controller has a hard drive on it, and that drive has an active partition on it, the system will want to boot from there.
If you have Win NT / 2000 / XP, and want to use the NTFS file system, you typically need to do partitioning from the OS itself. On a new compluter with a blank hard drive that means booting from your OS CD and going through the install process. If adding a new drive to an existing system you usually do this from inside the Disk Administrator utility.
This is another reason I love Ghost - when you clone a drive, it carries the file system along with it, and automaticly re-sizes the partition to fit the new drive.
Hope some of that answers your questions....
