First, as others have said, anything below 16 mil scouting (HS, College, or Int) carries increased inaccuracy. 14 mil, you're guaranteed to see inaccurate projections; 12 mil or lower, I'm going to exaggerate a little, but you're wasting money.
hockey1984 makes a good point about odd ratings; with inaccurate scouting you start to see things that don't make sense when you consider what HBD players generally look like. Pitchers with 48/92 DUR/STA or 28/100 left/right splits, things like that. I find you have to look out for what just looks out of place; it's a tell that your projections are BS.
And yes, pre-ranking the draft is, IMO, everything. No matter what settings you use, if you just draft off your master list you're going to pick up some players who are just placeholders. I try as much as I can to filter out players who I think have no shot at the majors. Like pitchers with control but poor splits, or second basemen who will never hit enough to get out of AAA. I aim to not pick career minor leaguers in the first five rounds.