Now, if you have build the circuit and connected to to the Latch16Bit board at the PC's parallel (line printer) port, you can access the the microcontroller's Flash and EEPROM using Atmelprg, a piece of software developed by me and available at no warranty under the GNU GPL.

Note: After downloading the source code, you need to manually configure the code before compiling it:
You may need to set some delays for port access using CONTROL_OUTPORT_DELAY and DATA_OUTPORT_DELAY in lpportio.h because fast computers may be too fast for the port, especially if the control port works in pull-only mode with a pull-up resistor to +5V. For my P1 with 100MHz, I need no data port delay but a 35 iteration for() loop for the control port. Expect much more for faster PCs. If in doubt, use large values or check using a DSO.
Next, look up your PC's parallel port base address and assign a proper value to parport_baseaddr in main.cc.

After configuring and compiling Atmelprg, you can start writing and reading the microcontroller's Flash and EEPROM using e.g.

atmelprg -load firmware.bin -erase -writeflash firmware.bin

Programming the EEPROM works similar using -writeeeprom.
In order to see if everything worked fine, you can read the flash content and compare it to the downloaded file:

atmelprg -load firmware.bin -readflash -compare firmware.bin flash

For a more detailed description on atmelprg, see the the software page.