And I had the same confusion when I was setting up my league. I was constantly referring to the FAQ to figure it out, but I think I have mine set up correctly now. Here's what I read in the FAQ:
"For every on-ice action, points are applied in every scoring category that action relates to. So, if a goal is worth one point in your league and a power-play goal is worth three points, a player scoring a power-play goal would be awarded a total of four (1 + 3 = 4) points."
On plus/minus rating: "Points: Points are awarded by multiplying the player's plus/minus for the game times the scoring modifier selected by the league commissioner. If the scoring modifier is two and the player records a plus/minus of four, a total of eight points are awarded."
I couldn't really find anything about negative point modifiers in the hockey FAQ, but the fantasy football one references that you can do it, so I'm sure it's the same in hockey.