Use Azure's ability to generate a .publishsettings file carefully. The capability is described here. Remember the Tribbles on Star Trek? Well each time you call that publishprofile.aspx page you get another management certificate added to all your subscriptions until the maximum allowed is reached. If you manage a lot of subscriptions, like I do, you can easily end up with a lot of management certificates to clean up.
To avoid this I prefer to generate my certificates using the script I blogged about. If you do use a .publishsettings file, Wade Wegner posted code showing how to use the file programmatically.