treebark,
Ask 10 people and you will probably get 10 different answers. Applications may have some dependencies on files in /Library and definitely have dependencies on items in ~/Library (Library on your Home folder). The basic structure that is installed by OS X has been thought out carefully.
Are you the only user on the computer?
I have a second user I created named clean and make no changes, additions or deletions when logged in under that name. This lets me more effectively diagnose the source of problems I create. If I can login as 'clean' and the problem disappears, then I know I have changed something inside the home folder of my regular login that is causing it.
A couple of other ideas to consider- do you want the second drive to be bootable, i.e. have a System installed there?
Consider partitoning the 200 GB drive, so you have a partition for big files a partion for another could be a place where you have an automated backup of your Home folder scheduled as often as you see the need.
Applications are available to all users, but the individual settings, serial numbers, prefs, caches, script, etc. are stored by user.
Another idea would be to have the second drivewith 4 partitions- a small partition for a base System install only. Partition 2 for your larger files- assuming that with a 200GB drive you have lots of large files, partition 3 where you mirror your first drive, and partition 4 where you backup you large files. Schedule the backup daily at night or for 2 backups- at night and at a time when you are away from your machine.
With OS X and 2 admin users, as long as you don't make changes to the System folder, you will have an very very stable environment. With a partition on the second drive with an OS X install only and a partition with your daily backup, you will then have tertiary redundancy of bootable disks. You will also have on System that is pristine, from which you can boot, a full backup of your first drive, and storage for your less frequently used files.
Craig
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