Hi Charlie,

Good question. The automatic global activation of the debugger for Arduino projects was a new feature for novice users in recent releases. 

It isn't well documented except in the last last release notes. 

The global activation can be switch off:-
"Tools>Options>Visual Micro>Micro Debug - Advanced>Always Use Debugger=False"

When "False" things will work pretty much as you requested by switch (Micro Debug=Full) in the project properties tool window for the configuration(s) (such as debug) that you want to enable debugging for.

If you don't already know (sorry if you do) you will see how to also create new configurations in the youtube video on the visualmicro.com debugger page.

Hope this makes sense

ps: One final small point is that "Debug>Start without debugging" should never compile and upload a debug version.