Hi,

Some information that I hope helps, if not please say

1)
If you have activated the debugger it should currently be in "simple mode", which means you can switch the configuration combo box on the main tool bar from "Release" to "Debug" then compile>upload. Debugging should automatically start. "Simple mode" has been added in recent releases, the docs need updating.

2)
For finer control of when the debugger is used you can switch off Tools>Options>Visual Micro>Debugger Advanced>Always Use Debugger". In which case the (Micro Debug) project can be used in combination with the selected "Confguration" of which you can also create your own. For example: Debug, Release, SpecialDebug1 etc.

3)
You are right that you do also need to see the project properties which contains (Micro Debug) but also lots of other debugger settings.

You have not stated which Ide you are using. In all cases you must click the project name in the solution explorer to see the project properties otherwise you will see the properties of whatever source file is currently selected (about 2 properties) 

NB: In recent Visual Micro versions, pressing the yellow question mark on the tool bar next to the boards list opens the Explorer and also the project properties.

If you are using a version of Atmel Studio prior to June 2013 you need to upgrade Atmel Studio otherwise the  Visual Micro project properties will not show.

Thanks