If I'm not mistaken in perplexing your question, Visual Studio stores two sets of window positions, one for the ones you are developing and one for when you are working. After you work, you can arrange the windows as you like, and they should remain in this position during subsequent debugging.
For example, in my IDE, I have the Error List, Output, Find Results 1, and Pending Changes windows at the bottom when I'm developing. When I run a debugger that changes to the output, locales, hours 1, search for results 1, breakpoints, call stack, immediate and command windows.
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