How to make a single form that works with an individual, and organisation and their Relationship in Wordpress
Sounds like you might need to set your Membership page up so that it is 'on behalf of' ie so the Membership is created for the Org, and the Individual becomes permissioned 'current employee of' that Org.
The 'on behalf of, settings are on the Contribution 'Title' tab. The profile it offers by default is a 'reserved' Profile (so is on the Reserved 'tab' on Profiles), but you can clone it, change the clone and use that if you don't like what the default one offers by way of fields.