Correct jumper setting for two SATA drives?

The jumpers have nothing to do with master/slave relationship since SATA only supports one drive per channel. I'd just leave them both on 1/2. Here's a bit of explanation:

http://www.overclockers.com.au/article.php?id=179581

If you're having trouble seeing them at POST, I'd check your BIOS settings to make sure the controler is enabled, and you're running in "enhanced" mode assuming you have IDE drives as well.
 
On these Western Digital drives, the jumper controls spread-spectrum clocking. You can read about it at the WD website.
 
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