I've been using BOINC for several years, and just got a BAM account so I can bring Mom's tower in on the fun. However, BAM hasn't detected any of my existing projects, even after I linked my BAM account to my primary computer's BOINC Manager, and even though at least half my projects have the same password, user name and associated email address.

You will have to go to the "My projects" page and click "Find account", account managers can't get the info from BOINC manager. And, you will have to use the same username, email & password for those projects which you want to manage through BAM.