the parts in missions have orientations too; good, bad and neutral.
so in your case chosing a mission with a read dot near it will make you more evil. So yes we know in advance.
orientation is not only based on the chosen skills it effects to a 70-75% and you have to complete missions in order to get more evil/good the fast way, that's what sprciufo said when I asked him.
I hope that bit of info helps
and as for what are they used for... well I guess it's just about our choices, only useful for rp? don't know that one really