External Hard Drive Options (Scratch Disk/Data)

It depends on how fast access needs to be to the scratch disk. The fastest data access speed is to your internal drive. If the scratch disk does not need to be particularly large (you work on something there and then move it off to your primary storage), you can even create a small partition on your internal drive and use it as the scratch space. Obviously, if you need it to be 1TB in size, that won't work.

You do get some benefit in efficiency if the OS and apps are on one drive (internal) and data storage (including the scratch space) was on a separate drive. But for uses that need really fast data access, the speed advantage of the internal drive versus even FireWire 800 probably makes up for the +scratch space+ being on the same drive, if you create a small separate partition just for that purpose.

use one of them for backup and data

Since you want to back up your data, you probably should not put the "data" and the "backup" on the same drive; if the drive fails, you've lost both your data and backup at the same time.

I'd go with one FireWire 800 drive with your scratch disk as the first partition. The second partition is your data storage. Then get a second large external drive and use it for the backup of both your internal drive and FireWire drive (minus scratch disk), using Time Machine (or other method). The second drive can be USB 2.0, since doing backups does not require super fast data access. USB 2.0 is fast enough for that purpose, usually costs less, and keeps the data load off your FireWire ports.

Getting one super huge drive would not be ideal, again because your backup is on the same drive as your data. If you lose that huge 2TB drive, you lose everything at once.

Even a drive enclosure that houses two drives is not ideal, in terms of data safety. Those enclosures are meant to be used as a RAID, to make an extra large single volume. If the enclosure has a problem, such as the power supply becoming faulty, that could potentially corrupted the data on both drives. If the data on one drive is the backup for the data on the other drive, you're risking loss of both at the same time. So if one of the two drives is a backup, I think it would be best if it is on a separate drive in a separate enclosure.

And if you want to reduce the data load over FireWire, it would not be a problem if the backup drive was connected via USB 2.0. Backing up data does not require FireWire 800 speed.

It does not run "non-stop." It runs once an hour for a few minutes, incrementally backing up anything that changed during that last hour. If you added a few GB's of video files during that hour, it will take a bit longer. If nothing significant changed during that hour, the backup run will be fast.

That is the power of Time Machine; your backup data is always up to date to with the last hour that your Mac is active, and it all happens automatically. In any type of data loss, whether it is human error or hardware failure, you can recover the system and your data to within one hour off the loss event.

You can also +go back in time+ to an older version of a file or to recover a file has been deleted (after you started using Time Machine). You can even restore the entire system to a state, for example, that is one week ago (or any backed up time and date), if you installed something a few days ago that messed things up beyond simple repair and you want to undo it.

Since it is only backing up incremental changes, your Time Machine backup disk will only get filled up based on your changes. You can exclude specific files or folders from being backed up. For example, if you use VMware Fusion or Parallels Desktop, those virtual hard drive files are large and change every time you run the virtual machine. So that is something you may want to exclude from the Time Machine backup. If you do not, every time you run the virtual machine, the multi-GB hard drive image file will get updated. Because it got updated, Time Machine will make another backup of it. Something like that can go through your Time Machine backup disk storage space quickly. Otherwise, if the size of the Time Machine backup disk is at least 2x the the size of the data to be backed up, you will be fine for many years.

If you ever want to not have Time Machine run while you are doing something sensitive, just go to System Preferences +Time Machine+ pane and turn it OFF while that sensitive action is taking place. Then, turn it back ON when you are done.