First... IMO never stack unless you absolutely have to. If you need to...

The bottom line (rod) is ran straight out the back of the boat with a larger lure/bait that will sink if the boat has to stop. Preferrably the upper line, ran off a side rod, should have a lure like a plug or slow sinking bait (cut plug by itself). If the fish hits the upper line, this should provide enough time to keep the extra rod in the water until position on the fish is made- vice versa for a plug on the upper line (it floats up).

Separation between the two lines is, as a rule of thumb, dictated by the length of line off the clip. Personally I run no more than 15 feet from the release. The reason is two-fold: (1) initial hooking power of the rod, and (2) comfort zone of the Black Box.

Lastly, both clips should be set tighter, with one being a tad more, to prevent premature releases from happening. If not, you could be in for a frustrating day on the water.