ArdUp - An Arduino Hex File Uploader

I have tried this and it works great!!! Problem is......Arduino IDE does this with ALOT less steps. If I wanted to upload HEX to say.....an Atmega16......what should I do???? I uploaded the Arduino ISP and attempted to upload the Blink sketch to an Atmega16.....but it only programmed the Arduino back to the Blink sketch. Should I look elsewhere for my purpose of programming a microcontroller through the Arduino?