If they show as 2 separate drives in disk management then the chances are they are 2 separate arrays.
As far as i Know Silicon Image does not allow you to make multiple arrays on the same drives(but 2 arrays from the same or 2 same controllers can happen depending on the board in use). Intel DOES allow this.
If its a single array with all drives it should look like this
One Drive (or array) and 2 partitions.

If its 2 arrays it should look like 2 drives.
3 (2 in your case) drives. Ignore the fact that i have only 500 gigs of my array partitioned. Its just faster for what i do.

Either way, you will have to make sure you unplug the right drives when you change things. Do not worry, if you get the wrong one. Power down put it back and all should be as it was again.