What is the preferred way to abbreviate amino acids?
In my experience neither is preferred. 

When simply presenting a protein sequence, e.g. in the context of a database of proteins encoded by a genome, then the one-letter code tends to be used. 

When showing an alignment of a DNA sequence with the encoded protein sequence both can be used, although personally I prefer the one-letter code for this too because I don't like squished-together text like LysAlaTrpLeu. 

In papers referring to an individual residue in a protein I would say that the three-letter code would be more likely to be used. 

When referring to a mutation (or,  rather, an amino acid substitution) you might see Leu129Gln or L129Q. 

And, by the way, I use L for ligand and have never found it to be confusing. If the reader of your text is sophisticated enough to know that L is leucine then I think they would be able to tell from the context that you were using L for ligand.