If you secure first and then use the database splitter, you'll end up with a
secure frontend, but unsecure backend. So you end up having to resecure the
backend. The solution to this is 'don't use the splitter wizard'. It's
easy enough to split manually and keep your permissions intact.
I would secure it and then split. To split manually:
Copy your database. Open the copy and delete all objects except the tables.
Open your original and delete all the tables/relationships. Go to File, Get
External Data, Link Tables and navigate to your copy and select all the
tables.
That's it. If you move the backend, you can use the Linked Table Manager to
refresh the links.