I think one of the most common mistakes that coaches make is putting too much time into Study Hall. I give all my freshman 4 minutes to start the season, and tweak from there. If they come back at 2.2 GPA or under on first midterms I will add more minutes, usually no more than a total of 8 minutes. If they have a GPA over 3 I will drop them down to 2 minutes. In general I give 4 minutes to all freshman all year long, and then many of them don't every require SH again. After the second term grades I give everyone 0 minutes. Since there are a couple of practices left but no more GPA requirements at that point in the season, any SH minutes in those last few practices are just wasted minutes.
I will start a SOPH at 0 minutes, and bump that up if needed based on first midterms. It is uncommon for an upperclassman to have any minutes in SH.
To answer your first question, I would start them at 4 minutes to be safe.
Pick one defensive and one offensive set, and put 20-25 minutes into each. With the rest of your minutes distribute them into categories that are important for that player based on their position and their potential left. Blue attributes mean they have >21 point of improvement remaining, black is 8-21, and red <8. In general its not a good idea to put more than 20 minutes into any one category. There are times when its appropriate do this, but we'll just stick with the basics here.
ATH and DEF are important, or "core", attributes for all players. The core attributes for the each position are pretty appropriate and what you would probably guess them to be. Don't be afraid of putting 0 minutes into unimportant attributes. If a PF has a red 6 PER rating, just give that 0 minutes and move on.
This should be enough of the basics to set you in the right direction, its not that hard once you get the hang of it.