Is there any difference in the end product when coding the atmel avr using arduino ide and in embedded c are there advantages with embedded c?
Arduino IDE is a tool used to write and upload code to the Arduino. Embedded C (or C++) is a language or a subset of the language. The Arduino IDE is provided with, and runs the GNU g++ - a C++ compiler - so that is the language you would need to write in. If you're asking for a comparison between C++ and the mythical "Arduino language", there is no Arduino language - it is C++. The Arduino IDE does manage a few details of the language for you to make it somewhat more beginner-friendly. The difference between the full-spec C++ language and C++ with a few shortcuts you can take with it in the Arduino IDE are what have given rise to to the myth of an Arduino language.
(Technically it is possible to program an Arduino in another languages by using an appropriate language compiler for your Arduino's AVR chip.)
Your profile suggests you're planning a career around software and the technologies it enables. In that case, it would be very worth your while to learn and write correct C++ and ignore the Arduino IDE's shortcuts, at least once you have a passing familiarity with the process. The Arduino IDE is well suited to learners but it has some real shortcomings that soon frustrate the serious student/programmer/engineer - meaning sooner or later you'll probably want to move on to a more professional level tool that won't hold your hand for you, but also won't hold you back so much. That transition will be easier if you know the full language requirements from the start, than if you have to re-learn some of them later.
Can you tell me how I should get started with using c++ with the Avr chip,and what software I need.
The only software tool you'll need is the Arduino IDE. It comes complete with the compilers, loaders, basic libraries, and sample programs. Despite my discussion of its shortcoming, I still recommend it as the easiest entry point for getting started. An Arduino Uno board is the only other thing you'd need and you'd be ready to go.
If you want to work with the bare chips, you'll need to provide the basic support circuitry that provides power, clock-pulse generator and USB to serial conversion. (This latter part is easy - it's called an FTDI cable and has the converter built into it). There are lots of articles on the web about home-building Arduino-compatible boards. You can make one on a printed circuit board, Vero board, a breadboard with plug-wires (instructive, but not too reliable because of all the plug-wires). Or one Arduino with a replaceable chip can be a programming host for all of your other (same part#!) chips. But note those chips will still need the support circuits to be able to do anything more than look pretty on your bench.