I assume that if you create fields, that point to a custom storage location, SEBLOD will search on that table, once the fields are added to the Search Type.
For seblod to be able to search 3rd party table, each record needs to have a corresponding entry in the #__cck_core table as search query always starts with this table and then joins 3rd party table - at least this is what it seems from my tests
To populate the #_cck_core table automatically you could create MySQL triggers that fire when you insert, delete or update a record in your non Joomla table.
If the database in which the non Joomla table resides is a remote database you might need to use federated storage engine. This topic might be of interest.