Users can be assigned an employer as a manager only when the employer's subscription status is "Full User." If the employer's subscription status is "Invited" or "Prospect," their name will not be available in the learner's dropdown even though they appear under the Employer logins for that Employer Organization.
Once the employer activates their account to "Full User" status, they will become visible in the learner's dropdown menu, and you can then assign them as a manager.