This is more of a ‘concept set’ question, but if you have custom source concepts that you can provide a mapping in concept_relationship table as a ‘Maps to’ to an existing concept, then you can use the ‘mapped’ option in a concept set.
However, the case you’re talking about: source_to_concept_map table just maps a source code value to a target concept. if you’ve created custom concepts in your CDM so that they appear in CONCEPT, then you can just add the custom concept directly to your concept set expression, and it will be used in the query.
Note that custom concepts are not unique across different CDM nodes: there is no protection that someone with a concept 2bil + 1 is the same as another CDM’s 2bil+1 concept. So caution when creating studies that leverage custom concepts. The durable approach would be to get the concept stanardized in the omop CDM and then map your custom source values to the standard concepts.