That's been very much like my experience, Chloe. There tends to be basically no useful documentation of name changes (except, perhaps, with the "legal" part -- the one that involves going to a courthouse or whatever). Every institution is different. With the university, it came about by talking to a computer help desk person, and I basically told him "I need to be able to use this email address for school-related issues, and I need the 'from' and 'reply-to' fields not to say what they do now." He said he could only change first names, and only to "nicknames," so i told him that my nickname is "Alyssa." He said he would put a request through, and magically a few days later, when I logged into the email servers website, it said, "Hello Alyssa." And I can now send and receive mail under an appropriate email alias (alyssa.lastname@schooldomainname.edu) The student billing office and the records department (grades, etc.) hasn't changed it -- but a library fine was sent to "Alyssa" and that's how it appears on the online university directory. Then there was the student medical center, which was a complete nightmare. I had to see a doctor for something (non-transition-related), and he wrote a prescription to "Alyssa," and an outside referral (also NTR) was for "Alyssa" as well -- which is how they billed me.
So ... yeah, bureaucratic magic. Don't even get me started on my research-related computer accounts.