How do you get rid of or replace the Microsoft Azure Media Services logo overlay (water mark) that is put onto dynamic packaged video? The following link shows the topic area: https://azure.microsoft.com/en-us/documentation/articles/media-services-dynamic-packaging-overview/
My html contains embedded code taken from http://amsplayer.azurewebsites.net/azuremediaplayer.html
It seems that you are attempting to use the iframe embed code on the "get embed code" section of the player. Please note that this is currently under development, as it is listed on the site: "this embed code is for demo purposes only. Do not use in production."
For your player needs in production, especially if you want to use the large amounts of API's available, you should create your own player page following the instructions in the documentation and by using the samples provided.
Specifically for the question regarding the logo, there is an API available to remove to logo and can be found in the logo option section of the documentation. This is the correct way to remove to logo using the APIs provided.