There are two things that I do 'wrong' or 'backwards'. The two items are creating new database schema's (not tables) and installing xml schema collection objects.
It just works better if I do these tasks in sql studio first, then incorporate them in my project with schema compare. Then, I can use schema compare to create deployment packages, without any help from sql server management studio.
My most often used setting in Compare Schema is "Block on possible data loss".
To find the setting to show the dialog box, look for the cog or sprocket graphic after the scroll.
Compare->Update->Scroll->Cog
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