IContentManager is a service implementation which itself accesses various IRepository instances to query and manipulate data in the database.
So, if within your module you are creating new database tables, you should generally create some sort of IMyModuleService which is where you'll import an IRepository<MyModuleRecord> and do the data manipulation.
Then, any other parts of your module that need to perform data access should just talk to IMyModuleService, rather than attempting any access of IRepository.
If you specifically want to access any Content Items from the database, just use IContentManager; you should
never directly talk to IRepository<ContentItem> since the IContentManager performs a lot of additional useful functions.
The basic message is that you should always keep all your database access in one place; this will make it far easier if you ever need to swap it out for a different storage mechanism or for testing purposes.