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You need to understand how the point system works. The player does not get points if his/her team wins the mission. You only get points for the units you personally destroy.

As for your second mission, you can indeed use a Destroy Ground Target for moving ships. Look at the screenshot below. I have a small test mission set up in the FMB.

There are two Blue ships sailing east. The Primary Target (which applies for Red) is set to a Destruction level of 50%. There is also a TimeOut limit of 20 minutes. So, if Red sinks at least one of the ships within 20 minutes, they win the mission. If 20 minutes is reached before Red completes the Target, Blue wins.

*The important thing to remember for this particular type of scenario is that the ships must remain in the Target Circle during certain critical times. These are:

A. All the ships must be in the circle when and if the first ship is destroyed. They can actually start the mission outside of the circle, as long as they enter it within this critical time.
B. All the ships must be in the circle when/if the TimeOut setting expires (in this case, 20 minutes).

Again, there are no points awarded for winning a mission. You need to destroy units to be awarded any points.

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