Is it possible to apply an existing contribution to an event registration?
Self service for supplementary payments for event registrations is not yet available in CiviCRM as of version 4.6.

As you likely know, it is possible to manually edit registrations to record additional payments, and to view all payments that have been made against a registration. When doing this it is possible to record notes to help document what is being done. As a work-around perhaps you could cancel the incoming supplementary payments of $50, and then apply them to the registration.

Alternatively, or in addition, we could set up a Make It Happen fundraising effort to get this into core.