When you say you've added the libraries to your project, do you mean you've added them to your compiler source directories, or added the library source files as "Existing Items" to the project itself?
Undefined references usually appear because the source files haven't been added as links to the project. If they're not added so that they show up in the Solution Explorer, Studio doesn't add them as build targets to the Makefile. The undefined errors are the linker complaining when it can't find the compiled object files (since they were never built to begin with). Specifically, this is in "Compiler and Linker Setup", Step 11 in our Studio 5 tutorial.
This means you must add the libraries in both places (C++ compiler setup AND as links/existing items to the project itself). If you've already done both of these things, I'm not sure what's up, as that's always worked for us. You can also check out our updated tutorial for using Arduino with Atmel Studio 6, though it uses the same basic strategy.
Edit: as an addendum, you can use Eclipse if you don't like the Atmel Studio workflow: http://arduino.cc/playground/Main/DevelopmentTools
There is the potential for some of the same issues, since you're still setting up a custom toolchain to replicate the Arduino IDE. Your particular mileage may vary.
AVR Studio 4 is based on Eclipse. It's pretty old at this point, but also has a well-defined workflow for that reason, so if you don't need the new features, there's a good chance it will work.
