In Data\Cfg gameplay settings scroll to the bottom of the file and change the MiscSettings to like they are below, it stops the popup that comes up asking if you want to attack, maintain current orders or submerge, as for your other problem, someone might come along who knows the answer to it.
[MiscSettings]
AlwaysAutotargeting=1,1,1,1,1;for warships, merchants, uboats, air and land targets