Not sure, auto-drafting gets done based on pre-draft rankings from the site, but I don't think they adapt them to your league settings. Most rankings are done half-PPR or PPR anyway so I wouldn't count on it.
In any case, do not autodraft. Watch a few YouTube videos of the top 50 ranked players (or top 20 ranked players from each position (QB,RB,WR,TE)) and then try to draft the players you like watching. It will make your fantasy season much more enjoyable. Even if you've reached for a few players in order to get them, I wouldn't worry too much about that in your first year. The rankings are most important in the first few rounds but if you like the WR48 over the WR35 in the 10th round, you don't do anything wrong with picking the lesser ranked player. In the first three rounds, keep ADP in mind and try to stick to it (or close to it anyway).
- Do not account for bye weeks
- Drafting two skill players from the same team is not necessarily a bad thing but make sure you get some variety to your team
- Don't follow runs (e.g. don't pick a QB just because the 4 picks before you were QBs)
- Read, read, read about draft strategies