The bishop pair is usually stronger than B+N or N+N. While doubled pawns are usually weaker than two adjacent pawns. My advice is to look at the pawn structure and king placement to guide your decision whether to allow your opponent to exchange a bishop for your knight and leave you with a doubled pawn. Let's start with the Spanish system
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1.e4 e5 2.Nf3 Nc6 3.Bb5 a6 4.Bxc6 dxc6
practice has shown that black can handle this type of pawn structure by following the correct strategies. Next, in the Trompowsky attack
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1.d4 Nf6 2.Bg5 h6 3.Bxf6 exf6
the light squares (d5, e4, f5, f7 and h5) become sensitive for black and white is better.
Next, the following silly example
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1.d4 Nh6 2.Bxh6 gxh6
shows that black simply cannot accept this sort of pawn structure to get the so called "bishop pair advantage". I would recommend to study and think about the bishop pair versus B+N or N+N situations. As well as delve a bit deeper into pawn structures and weak squares. Here are a few possible guidelines
- Do not allow a doubled pawn that makes your king weaker
- Do not allow a doubled pawn in the endgame unless you are sure you can hold it
- The bishop pair gives an advantage only if you know how to use it (practice!)
- An enemy knight placed in front of your doubled pawn can be a real pain