So, I've never run a game before and I understand that this game kind of leaves it up to the GM on how to handle things but there are a few things I'm not quite getting.

1. Features for NPCs. For example, one of the four horseman has mutiple positive features and some negative. How do the negative features work? Do they apply to that creature or towards the PC when encountering them? I know that PCs could encounter these creatures without combat and I don't know how to resolve that either.

2. When to use opposed checks vs actual combat or non-combat checks?

That is my biggest question. I understand combat and everything else, just that confuses me.

Answering number 2...

I interpreted opposed checks as non-combat decisions. For example, one player suggests one action for the group (filled with PCs and NPCs), while another player suggests a different action. Both players would role for the appropriate stat (in the above example, social). The player with the most successes would convince the NPCs that their suggestion was the best plan of action.