Okay, this has been a question that has been asked over and over in this forum and I have figured out how to finally do it.

Here is a step by step guide to remapping the Mupen64Plus keys:

Step 1:
Open the data folder.
Press windows key+r and type in C:ProgramDataVizzedVizzedRgrPlugin

Step 2:
Navigate to the Mupen64Plus folder.
This will be located in the User-(your user#)Mupen64Plus folder
Example: My user # 374776 so mine would be located in User-374776Mupen64Plus
Most of the time, there will only be 1 folder with a user number unless you share a computer with someone else with a vizzed account.
In that case, simply go to your profile and look at the numbers in the URL to see your user number.

As you can see on my profile page's link, its the number after "id="

Step 3:
Open the InputAuto.cfg file in a text editor other than notepad (wordpad should work fine)

Step 4:
Here is where it gets slightly difficult, but nothing too difficult if you got this far.
You will now edit the keys using the key codes for each key you want to remap.
Use the list at the bottom of this post to see all the key codes.

Example of how to enter a key code to change a mapped key:
Here I use the Start key, which by default is mapped to Enter:

In the example, the key code is the number in the parenthesis (13)
For my example, I will remap the key to the 7 key.
This is represented by key code 55
Here is what it should look like after you change it:

As seen above, the number is changed from 13 to 55, changing the Start button from Enter to 7

Step 5:
After you have remapped the keys as you wish, you will need to save the config file.

Click file as shown in the image above then click save.

Step 6:
Close the editor.

Step 7:
We will next need to set the file to read only so it doesn't revert to the standard config.
To do this, you need to right click the InputAuto.cfg file and click properties.
In the General tab, you will see a check box with "Read-only" next to it.
Check the box and click OK.

Step 8:
Close out the Mupen64Plus window, start up a game, and enjoy with your newly remapped controls.


Key Codes:

vanelan :
How do we remap the controls to make it work with say an XBox controller or something of that nature?

therealsilvercdccd : Well, first question, does it work with windows? 
Press Windows key+r and type in joy.cpl and see if it shows up in the game controllers panel. 
Click the controller and go to properties and make sure its working properly. 

Let me know. 

vanelan : Yes. The controller works. I have it set up to work with the 1964 emulator. But I would prefer to use it with the Mupen64Plus emulator.

therealsilvercdccd : Does it work at all with the mupen emulator? Typically,  the controllers work but the controls need to be manually changed in the configuration file. 

vanelan : No. It's not working at all with Mupen64Plus as far as I can tell. How would I change the controls for the controller?

therealsilvercdccd : You would have to open that file as described above. 
Is that the only controller you have plugged in? 

vanelan : Yes it is

therealsilvercdccd : Press win+R and type in joy.cpl
Click advanced and choose the xbox controller as the preferred device and click ok.

vanelan : Did it. It's still not working with Mupen

therealsilvercdccd : Check to see if the config file has this in it:

vanelan : Yep. It's got all that

vanelan : I found that part, but how would I set it up so that the PS3 d-pad would be the C buttons instead of the R3 stick?
I'm using the Better DS3 to connect my controller if that helps.

DLCJRpc : What does the controller show up as in Windows? 

vanelan : Controller (XBox 360 Wireless Receiver for Windows)

It did not work. I tried to reconfigure it for different keys on my keyboard, But they did not change.

imamonster : Did you set the corresponding keycodes and not the letters themselves?
Also, did you save then write protect the file?

just took a look at that config file and... *facepalm* could i just get some info on what the default config is in a less text mountain format please? i mean, thats just a single LONG string of text as a text wall, i can't read it.

ok ok, left shift = A, left ctrl = B, Z = Z... enter = start, arrow keys are the...d-pad, i think? not sure what the joystick and c-pad keys are yet.

treos : That will happen if you open it in notepad.
You need to open it in wordpad or another program that can read formatting properly.

huh, ok, well i managed to figure out the default controls not long after posting here actually. funny thing, the default controls actually seem to be easier for me to use than how i usually set them in the 1964 emulator (might have to change them to match the mupen settings next time i use 1964). those i listed in my previous post actually make it fairly easy to play, yay for that good news.