when you have the entire map(the first few scouts should give you that). i manualy set the routes of scouts totake the path where they spend the least amount of time in gravwells. also, keeping a scout in ucgw's is a nice way to keep an eye out for sneakieness

Research Selective Phasing for Vas Navagators and park them in a star's gravity well. Turn off autocast and turn on the cloak. Indefinite intel on the star

I don't do anything diffrent then you do i find that it works well and if i ever have extra resources that i can spare i build scouts and send'em out. But if you want to be more advanced and start doing more effective managment you could do some research into it and manually order them around, but i find that, that is too much work and spamming them works better .

Yeah, I can't count the amount of times I make a new scout, put it on auto-explore, and the first place it decides to go is the pirate base...

Early on I use auto explor, then (if I can) I make a few and send them to the star, wormholes, places like that and let them sit. I always try to keep a few on auto explore throughout the game and sometimes spam like 10 and send them all into enemy territory ahead of my fleet before an attack

Sometimes a colony ship is the best scout.  Some of the best intelligence comes from asteroids or gas giants with obtainable resources.  The ai tends not to disturb these once you aquire the extractor.  This provides not only resources but free real time intelligence for the rest of the game.  This is why it is important to build more than 1 colony ship early to quickly capture these positions. 

I usually build one and give the scout orders to jump to enemy planet, then jump back to friendly side. Obviously what happens next is I select all units on the friendly planet for an attack...