I am working on a project which requires the main usb interface to an atmel chip (32u4) to be USB-C. In this case If I only connected the traditional usb 2 pins (D+, D-, +V, GND) to the atmel usb driver would this function properly? I Am worried it might draw power from the device instead of supplying it (because I know USB-C can be used for charging computers on the new apple computers for instance. I do have a transistor circuit which switches power away from the battery to the usb bus if the usb bus has 5v (and this works with normal usb) but I'm not sure if this would work with USB-C.
To make correct Type-C connection to your battery-powered Atmel MCU, you need to ensure four things:
Make sure that your battery is not connected to Type-C VBUS, never. So a transistor switch (or better some dedicated power-path/charger circuitry) is required to have the device powered both ways
Connect both sides of data lines, A6 with B6, and A7 with B7, to D+ and D- wires. This will make the connector flippable.
Connect two separate 5.1k resistors to both CC pins to ground.
Make sure that your MCU doesn't initiate D+ pull-up until it sees the VBUS coming from Type-C receptacle when a cable is attached to a USB host. The AtMega32 MCU has a dedicated VBUS sense pin with proper voltage tolerance, so no special logic-level translation (usually a divider) is needed.
Having pull-downs on CC pins signifies that this is a USB device and power consumer (sink). No other "USB link partner" will attempt to draw any current from your device. Then everything should work just fine.
Yes, that would be fine. I have used USB C on a Cortex M4 in exactly this way.
Have a look here:
Your power circuitry will help in terms of how the 5V from the outside world is connected to you board. I've even had unit where I don't do anything with the incoming 5V.