I don't remember where or when I learned this, but you can mount your main battery guns on the top deck. It really helps with this mission. Seriously, don't use the silly casemates, drop a big ol' cannon or two right on the roof. At least that way it can turn a full 360 and shoot.
At least in the video it looks like auto-avoid is affecting your ship. Your ships will automatically maneuver to avoid collisions with other ships. You can avoid this by using manual rudder control in the bottom right side, just right of your speed selection. That will force the ship to maneuver, whereas right clicking will use AI rudder, but will avoid collisions