I have made a script that changes bounties based on when you are wearing a garment, like the Cowl of Nocturnal in Oblivion. The script I have works perfectly for me but I don't get the "xxx bounty added to xxx" message when it changes. What do I need to add to get this to appear? Or make my own notification messages.

Do what I do when making a mod, plagiarize. No, don't steal resources and call them your own.

Open up the game in the editor, find the Message box and see how it is triggered and how the text is applied. Probably have to look at the scripts that are related to Bounties to see what is triggered. Find that object, see how it works, and apply it your mod. I never build anything from scratch but always copy other work or techniques from the game.