Hi,

Only partially in Visual Studio. You can use the arduino/atmel toolchain in VS with Visual Micro but without the arduino core.

If you add a main.cpp to your arduino project then you override all the arduino stuff but keep the rest of the build/upload.

You can click "vMicro>Toggle Hidden Files" to see short cuts to the current arduino core. In the list will be the original main.cpp that arduino loads from. You can override any part of it however you will need to stay in release more and not attempt to debug

I the long run atmel studio might be easier for this type of project.

Hope this helps.