This is a great question.
You should only have one developer account per organization. I recommend that you apply for an ‘organization’ account as opposed to an ‘individual’ account.
Once you have that developer account set up, you will be able to set up different Twitter apps. You should have one Twitter app per use case.
In your situation, you should probably just have a single Twitter app. Then, you will use the 3-legged oauth process to authorize your application to make requests to the statuses/filter endpoint. You can authorize your app to make requests on behalf of as many users as you’d like.
So at the end of the day…
You should have one developer account that manages all of your Twitter apps.
You should have one Twitter app per use case.
You should then authorize your Twitter app to make requests on behalf of your users.