Hi, thanks for playing! ^^
1) Yeah, you can definitely use a differently coloured die. I think in that specific case (Resistance rolls), you are only looking at the best result rolled, i.e. just one die. If you use the result of the Strain or Covenant-given die, you would not gain Bloom or Scourge if you use the result of that die. But take note that this may mean you'll be choosing a worse dice result than you normally would like.
2) I think I might have actually not mentioned it lol, so that's on me. Yes, you choose one Mystery (magic discipline) at Mancer creation, and after that you choose one spell from that Mystery that you know already. If it feels too little, knowing two spells works too, but they must be from the same Mystery.
3) By duet games I'm assuming you're playing with yourself + one other player? I don't see why not - if making other characters being controlled by the same person, you would simply make a sheet for them as you would a normal character. For ease of use, the main things to focus on are what spells they know + their Bond points + their Action scores. Their Mancer abilities can be focused on less if you're aiming to streamline remembering & controlling multiple characters at once.
Hope it helps, and don't hesitate to send your stories about your game experience! I'd love to hear them.