Need help finding inactive users in my database I am trying to figure out how to get this figured out.

Problem:

Users of inactive customers are receiving scheduled maintenance notifications

Indicators: 


Organizations have a custom binary field to indicate if they are Active
Users have two binary fields to indicate if they can access the
system


Solution: 


Identify any users that have their Active and/or CanLogIn values set
to 1 AND
Are associated by OrganizationID to an Organization with the custom
Active field set to 0 (zero)
You can find the logins on an instance by querying sys.server_principals and checking the is_disabled column to know if they are still useable.

SELECT name, type_desc, is_disabled
FROM sys.server_principals
WHERE type IN ('U','S')


The other notes you have in your question though indicate that this request is based on an application table. You state things like Active and/or CanLogIn values set to 1 and associated by OrganizationID to an Organization. All of that would tell me this is custom tables within an application database. Which unless you provide the table definition(s) there is not much we can do to help.