So it sounds like what you want is a many-to-many polymorphic. Many People can have many preferences. Many Organization can have many preferences. So you need 2 tables.
preferences id name
the "pivot" table
preferenceables preference_id preferenceable_id preferenceable_type | string "Employee" or "Organization
The 2nd part of your question I'm a little confused about but it sounds like you can do that as pivot data inside the preferenceables table
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