The goals of this program is a nice small, fast, reliable and simple to use program.
You can set your settings according to your project. this steps will execute after you push "Auto Program" button on the main window or press CTRL P shortcut.
From the latest version you can override chip signature check (for example for ATMega48 and ATMega48PA chip signatures are different but with overriding sign check you can program this chips truly). You can change programing clock speed too.
Fuses and Lock window help you to set settings for AVR chips. All settings are documented and can select easily from combos or set directly from check boxes.