You can also turn on SHOW POTENTIAL COLONIES, this is the forth button above the mini-map. It will place a pulsing red to yellow circle around systems that have planets that you can colonize. As you research more techs that allow you to colonize more planets, more cirlce will appear. They will disappear when you colonize them.
As for turning automation back on after a scout explores a sector, i would say it depends on your play style. Iam currently playing even clusters. I also play cannot colonize beyond 2 sectors, abundant colonies, and I start the game building 9 additional scouts, for a total of 10. So if I assign 1 eash to my home system and the 8 surrounding sectors, leave two on auto. Again, depending on your galaxy map, that may give you a lot of systems scouted and take quite a bit of time. By the time your scouts are done, you may have your hands full with monsters, pirates, and other empires, not to mention running our own empire. You don't want to forget about those scouts and leave them sit for game months. If you want to make sure a certain area gets scouted next, then leave enough scout with their auto turned off so you can reassign them, just dont forget about them.