What is the best practice to add a database index to a custom table?

You should be able to follow the same guidelines that are here, just use your custom module's module name:

https://support.sugarcrm.com/documentation/sugar_developer/sugar_developer_guide_13.0/data_framework/vardefs/working_with_indexes/

FrancescaS

Does this allow us to add an index to the _cstm table if the fields are in the _cstm table?

Or does this only allow us to add an index to the main table for the module?

I have the same need.

From my experience it's not possible to handle indexes on _cstm tables through upgrade-safe code

I have the same need.

From my experience it's not possible to handle indexes on _cstm tables through upgrade-safe code