I need a way to enable a secretary to have full (read and write) access to her managers calendar and email. They both have BB 8800s and I have a BES with Lotus Notes backend.

Have the manager delegate access to this person in their mail file preferences. Your Lotus Notes administrator should be able to easily set this up if the end user is unable to do it on their own.

The secretary will not be able to get the manager's e-mail and calendar on her own Blackberry however. She will only have access through her Lotus Notes client, or iNotes.

That's correct. Having that functionality on their desktop is easy. No way to accomplish it on a Blackberry, though.

Delegates can have access to their boss's calendar/contacts/tasks/notes on their BB's with Exchange and BES (our executive assistants are set up like this). However, you can't sync wirelessly like this. I have no idea about Lotus Notes.

There's no good way to grant access to another's email on a BB.