Side by side facing the same direction and direct radiating is good. Symmetrical side-firing with one towards the hull and one towards the interior pass-thru wall is good as long as both woofers' output is unobstructed with no reduction in radiating area along each path. One fore and one aft, in other words, one positioned in front of the other is very bad.
Two identical woofers sharing the same air space is fine as long as you adhere to the combined displacement. A partial division by a front to rear stiffening brace is a good idea.