1)If there are no attacking destroyers, and a defender has more than one sub being attacked in the seazone, he should be able to submerge only some of the subs and fight with the others . At the moment this is not possible: the defender is able to submerge either all the subs or none.
2) If you have sufficient production capacity, you have to mobilize all the units you have bought. It is written in the faqs. Now you are able to hold back units even if you have production capacity.
Hope to be solved in the next version.