USB C atmel chip interface
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.