Well, first thing's first, non-combatants don't like being group with combat forces. You sure you're adding the scouts to the combat group to begin with? Unless the group is hotkeyed, you have to reselect the scouts every time. Not sure if that's your specific problem though.
Try searching for Starships in the galaxy menu. Any planets that have a number over them, go to planet view and use the right hand icons to find their silhouette.
Ah, the eternal issue. Personally I like setting up enough defenses that I only have to get involved when an exo wave or Champion shows up. Still, after a few games you'll learn to keep an eye on the ticking timers. You should still officially request the auto-pause feature on
Mantis, I can see that helping a lot of new players.