Granted you have either bought a complete board from me or followed my DIY setup guide to a 'T', you are ready to use your Programmer/Reader board.
You'll need the software for the PC-side communication. You can find it on the author's site here:
http://www.reinerziegler.de/readplus.htm#Home made programming systems
Click the link "GB Cart Flasher programming software V1.1" and download the files. Install it where ever you like.
If you are using Windows 7, you may need to run it in compatibility mode for Windows XP. I do and it works. If you don't know how to do that, right click on the shortcut and click properties, then check the box for compat mode and choose Windows XP. Then hit OK.
Plug in your device and then start the program. I like to make the window larger because there is a readout of what is happening. The readout should state that the program has started, whether it finds the device and then what firmware version is running on the device.
Plug in a cartridge and hit "Cart info" to make sure that the cart has a proper connection. If everything is unknown and there is no "--ROM/FLASH content information" then remove your cart, clean the contacts and try it again.
Eventually, you should get a good connection and it will look something like this:
take this info and set the boxes on the left to reflect it. In this case, we can see that the ROM is 512KBs, the RAM is 8KBs and the MBC is MBC1. It may not be necessary, but I will change the MBC to MBC1 rather than Auto just to be safe. Set those boxes, hit "Read Flash" and designate a save location.
The progress bar starts moving and the readout states that it is reading. After a time depending on the ROM size, you'll see ">Success!"
Follow the same method to backup your save files but hit "Read RAM" instead.
As you can see above, I backed up both files. Save files are not compatible with all emulators, but they are good to keep on hand since the internal batteries are dropping like flies now-a-days.
The method to write ROMs and RAMs is the same, but just with two different buttons.
Plug in your "flashable" cartridge and click on "Cart Info" again. You'll either be given the contents as before or you'll be given the "Cartridge is blank, damaged or not connected" message. Hopefully, it is just blank. ;)
In any case, hit "Erase FLASH" and wait for the process to complete, otherwise you will get a timeout error if the ROM is already full.
Once it succeeds, press "Write FLASH" and browse for your ROM. It will go through the process and complete.
Thanks for reading and Enjoy your gameboy!