I use VB regularly and have found it quite stable. I feel confident to address at least a few of your questions:
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Is there some way to change the standard settings with which a new VM is created?
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Once you create a new VM, you can go into the settings for that VM (click the VM in the left windows and select settings at the top of the right window) and a settings dialog will appear. I commonly customize the size of the virtual HDD and amount of RAM. You can also change the settings of an existing VM, as long as the VM is not running at the time.
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To not have them open in a new windows but be able to switch just using the overview window on the left in the main virtualbox window?
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If I have more than one VM running, I normally switch between them just as I would switch between application windows.
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Whats the best way to use Cinnamon Desktop and unstable debian sources?
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In my opinion, the same way that you would if you were on bare metal.
Good luck.