The FTP or HTTP bandwidth is probably going to bottleneck unless you have a really fast upload. The 1TB will probably be marginally faster because of its higher density, but it probably won't be noticeable. Summary: probably doesn't matter.
The best layout is to use one of them for backups (unless that is otherwise managed). Try to figure out a way to recover quickly if the main disk fails.
What's the specs of each drive? Put the one that has a faster RPM / bigger cache as primary and use the other for backups.
If they're the same specs wise then don't matter. If you're concerned on I/O then buy another 250 or 1TB and use RAID 1 or better yet buy the velicraptors or SCSI / SAS drives.
How important is the data? I see two options, use the 250 a primary and create .tar.lzma's of the entire drive however frequent you like to the 1tb, or use the 1tb as primary and backup the important data as a .tar.lzma to the 250.
Are you using linux? I can give you a basic idea of how to do the backups.
The 250GB drive is being used as a backup. I just manually back up the important files every now and then. Nothing is so critical that it'd be a disaster if I lost it.
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