Glad you like the mod! I understand the mechanics of the mod may not be intuitive to understand so I would advise you to read the TIPS & TRICKS, most mechanics (including recruiting private citizens) are explained there.
In regard to your questions:
1 - 'Recipes' that use private citizens (ie. training/recruiting) will periodically search an area of a 100 tile radius to see if there are any private citizens around and grab them automatically. You can force this procces by opening and closing the building that uses the recipe.
2 - Private citizens cannot be controlled. Recruited colonists can by using the colony selector tool (default SHIFT+C).
In regard to your suggestions:
- I suppose I could consider making this an option, but I have a question first. Why? Are they annoying to you? Too loud? Too frequent?
- Sadly that is not possible, otherwise I would have done it. Units in factorio can only have running animations and don't have idle animations. If you look closely at biters you can see that they too don't have idle animations, they just get stuck in the running animation frame they were in when not moving. It sucks but I have no solution for it.
- Well we do have the Factoriopedia now, but I put most of the important information into the TIPS & TRICKS. Transfering the info to the factoriopedia is a good idea, but I would only do that if this mod is properly finished and only needs polishing.
