Can I do this and still program it with the arduino IDE
Yes it is pretty easy, maybe you have to make a new entry in the programmer.txt
I have succesfully used both USBasp programmer and Pololu programmer with the Arduino IDE take a look at this for example.
But that was until I learned about TinyISP
http://arduino.cc/forum/index.php/topic,123388.30.html
which makes debugging much easyer