You can also check the YouTube Guide.
This Guide is for the PokEdit QR Gen. But there are other more simple ways to use PokEdit QR without the need for PKX files:
Event QR: Event QR Guide
Send Event Pokemon to your game with QR codes. Now PKHeX or PKX files needed.
QR Cloner : QR Cloner Guide
Clone Pokemon in your game with three different cloning methods.
QR Learner : QR Learner Guide
Learn your Secret ID and Trainer Shiny Value with QR codes.
Item QR : QR Item Guide
Get x999 of many items using Item QR.
Now onto PokEdit QR Gen Guide....
This guide might seem long, but it's not really. I'm just documenting every step with pictures.
Also sorry, my system is Japanese, but you can use this with any region and this should still be easy to follow.
- This will not work on a "New 3DS".
- This will not cause your game to corrupt (but be sure to only use your own QR codes or ones offically from PokEdit.
Pre Step: Delete 3DS Web Browser History & Cookies

Select the wrench:

Select and Delete your browser History & Cookies
(these two options will probably be in English for you)

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Scroll down a little to see these two options. Click on both of them and say you want to delete/clear them.
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Create a Pokemon QR
Use a program like PKHeX to create a PKX file. You can also get PKX files to use from here: PokEdit QR Forum

You can create your own PKX File to use with PokEdit QR using this program. If you're not sure what you're doing then you may want to ask for help or get your PKX files from a trusted source though.
You can use this program to open PKX files, make some changes, and then resave them to use with PokEdit QR.
Get a standard Breeding Template Here
Save the PKX file to your computer. You'll need this file

Go to PokEdit QR and upload your PKX File
You can select file or drag and drop it into the box.
Once you select your file you will get a QR code like this:

Now onto the real injection process:
Make remove in Box 1 Slot of of your PC:
If you don't do this you will override whatever Pokemon is there.

Back out of the PC and Click the HOME button on your 3DS

Press the L & R buttons at the same time to active the camera App.

Scan the QR code you made ealier with your 3DS camera

Select OK then OK again.
You'll then be taken to the browser on a page like this:

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If it says Sucess wait on this page until your browser crashes!
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Then click OK:
Now go back into your game.
Enter the PC and check Box 1 Slot 1.
Your Pokemon should be there.

Congratulation!
Please make sure to share the love. If you have a QR that is great please share it in our PokEdit QR forum!
Huge thanks to lunarcookiesfor making creating the original!
What if this didn't work?!?!?!
- Did you delete your History and Cookies?
- Are you using a "New 3DS"? That will not work.
Thanks to lunarcookies for building the original system. Use the original QR scanner here.
Go make inject some Pokemon!
PokEdit QR