It sounds like you were able to resolve your initial issue. Thank you for letting us know.
I am assuming that you are referring to the error messages shown in the Output pane of Atmel Studio in Screenshot_1.png. If so, it looks like you have another main defined somewhere in your project. From your screenshot, it looks like there are some Atmel Software Framework (ASF) files that got added to your project, and those are probably causing problems. How and where did you install the Pololu AVR library? Did you follow the instructions under the "Programming in WIndows with Atmel Studio" section in the Pololu AVR Programming Quick Start Guide?
You first need to successfully compile the project to generate output files like .hex and .elf; if Atmel Studio was unable to compile the program, I do not expect it to create new output files in its project directory. However, you should be able to find the .hex files for each the AVR library's examples under a folder there called, hex_files, in C:\libpololu-avr\examples\atmega328p and load it onto your 3pi.
#include directive tells the preprocessor to search for a specified header or file and replace the directive with the entire contents of that header or file. (For specific details, see this page about the directive on the MSDN website.) If the library was installed properly, you should not need to restructure the contents of the library to get it to work in Atmel Studio. As I said before, when you compile a program successfully, Atmel Studio generates a .hex file that you can load onto your 3pi.