With a hardware programmer, you still need a program to utilize it. There are several programs that you can use, but I’ll only mention avrdude here.
avrdude is quite powerful and flexible, and should be sufficient for most, if not all, development purposes. To use avrdude with the ET-AVR JTAG USB programmer, your command line should begin with the following:
Obviously, you should change the -P option to reflect the actual USB-serial device. You should also append additional options and commands to upload/download various memory type.
Two options that are worth mentioning is -u and -V. If you are going to program the fuse bits, you should use both of these options. These options together prevents avrdude from verifying the locations programmed after each byte is programmed. This is necessary because the fuse bits (if more than one) should be programmed together and not individually.
For all other write operations, don’t use these two options so that avrdude verifies as much as it can to ensure proper programming.