Hi there,

We do plan to extend to created the correct project type for sam projects. It currently defaults to avr8 however Visual Micro will work with the sam format project.

To create an arduino project you do not have to use the standard "Sketch" menus. You can create an empty sam in a folder of the same name, then add an .ino file of the same name. This is all that is required for VM to kick in and do it's stuff. If you then renamed the .ino to something else VM would go silent and allow the normal Atmel stuff to work.

There is a huge difference between ASF and Visual Micro. When Visual Micro is active only the intellisense features of Atmel are used, the entire build process is overridden to be Arduino compatible which does not work the way Atmel normally works, Atmel scripts, libs, project settings all become irrelevant.

An Arduino project must not include a main however the best way to use examples might be to call whatever the main called from the setup() or loop() or the master arduino sketch.

Libraries can only be included as real arduino libraries, you might need to read up on that. 

For Arduino compile, project source files must only exist in the sketch folder, sub folders are not compiled (these are all arduino rules). Sources in other folders will be ignored.

We are considering supporting an Arduino/Atmel hybrid in future versions which would allow some ASF stuff combined with Arduino but right now we are only Arduino compatible with a few variations.

If you create an Atmel project manually you can delete all the scripts that are created within the project by Atmel and would need to move the src files into the main folder.

I hope this helps, I haven't had much time to play with this so hopefully the above rules will give some pointers. Feel free to re-clarify or ask other stuff. Sorry