What ideas am I missing in this position
In this position, not only is White down a pawn, White also has a backwards e pawn, which Black can easily exploit with its knight, queen and bishop. Especially since the Black bishop is dark-squared, the e3, d4 pawn structure can be easily broken. The White King is also quite unsafe, as what @briantowers has mentioned, as there are no pawns are dark-squares, leaving empty holes in White's position which Black's bishop can easily sneak into.
are the positions of the queens really that important?
In my opinion, at the moment the queen's positions are not really important, yet. Especially in the endgame, well placed queen's can lead to one's advantage e.g. controlling more squares, controlling the center, more space to attack.
What can I do to avoid this kind of miss-evaluation in the future?
When looking at a position, always evaluate the following in order (not 100% accurate)
- Material advantage (whether one side has more pieces than the other) (for exceptions e.g. rook vs N+B, evaluate the position and placement and if they are enough to compensate for the 1 point)
- Positional advantage (positioning of pieces)
- King safety (under positional advantage, in this case, where Black's king is quite safe, while White's king is vulnerable due to the dark-squared pockets in White's position
- Attack possibility (under positional advantage as well, King safety is usually top priority, unless your attack forces the opponent to do something else rather than continuing the attack on your king)
Evaluation of position
After looking using lichess stockfish analysis to make the best moves at depth 22-23, I came up with this
[FEN "r1r3k1/5pbp/p2qpnp1/3p4/3P4/2N1PB1P/P5P1/2R1QRK1 w - - 1 1"]
1. Na4 Rxc1 2. Qxc1 Bh6 3. Nc5 Rc8 4. Qd2 a5 5. Re1 Qd8 6. a4 Bf8 7. Rc1 Ne8 8. Be2 Bh6
As you can see, Black is constantly putting pressure on that weak e3 pawn, and White has no choice but to try to protect it. Additionally, if you're wondering, Oh, but White has an excellent outpost for the knight!. You're not wrong, but the problem is Black can easily kick it away or force a trade. Black has enough pieces (rook, bishop, queen, knight) to attack that piece and can force a trade whenever Black wants. Plus, the White knight is not really doing anything but sitting there.