There's two versions of the software. Latest Markus version would be
1.15m. Karl-Heiz's firmware has the version 1.11k.
I never used winavr, but with Avrdude and GNUmake installed you can do it all from command line. First you need to know your hardware. The most important stuff being:
You have an atmega328p so -> PARTNO=m328p
What type of LCD do you use?
Is there a crystal on your board?
Do you have a bunch of transistors in your battery power circuit?
Is there a voltage divider measuring the battery voltage?
The pocket avr programmer is based on the usbtiny so -> PROGRAMMER=usbtiny and PORT=usb
According to that, you'll need to set the Makefile options. Did you read the
Makefile and the
documentation? You'll also need to be more specific about your problems. We can't really guide you through what to do, if you just say 'I don't know winavr'. Try it, and then tell us, what did and didn't work. Be very careful with the fuse bits or you risk bricking your controller.