If I understand correctly, you need to go to s2Member / General / Login/Registration Design and under Login/Registration Page Customization (optional), select Yes… under Enable This Functionality?
This should make logging into your sight always go through s2Member. I have two ways for people to log in (paid POA Members and free “Bulletin Delivery”) and have a two custom logins - the POA Members is a customized s2Member Wordpress login (https://poa4us.org/wp-login.php) while the free uses a page (https://poa4us.org/membership/log-in-page/) using a short code.
Also, something which might be helpful is using the s2Member Widget and short codes to show login information (membership level, EOT date, street address, etc) in the sidebar and footer widget areas.
I took this site over a little less than an year ago to add s2Member and get their 17000 member records organized and imported - that was a task. I will be making changes to the site cosmetically in the near future.
Hope this helps.