I want to also import sqlwatch_logger_whoisactive table into the central repository. This table is not listed in [sqlwatch_stage_repository_tables_to_import].

What values do I have to insert to also import this data into our central repository with use of SQLWatchImport.exe

This procedure [dbo].[usp_sqlwatch_repository_populate_tables_to_import] populates the tables to import. I notice there is a comment:

-- exclude tables that break the import that need fixing:
insert into @exclude_tables
values	('sqlwatch_logger_whoisactive'),

but I am not sure why they were breaking the import. I think this is from when we did import via Linked Server which does not support XML. You can try it in your config and see if it works.