Project64 2.2 (and every versions before) doesn't support 64DD at all, so you need a development version that you can find on the Download page.

You can either download the original dumps, or the cartridge ports (but I don't recommend it); both work.
I will assume you know how to set the controls and stuff. What I'm interested to talk about are the Graphics plugins, the N64 Mouse support and how to load 64DD IPLs, required to play the games.

This page will assume you are using Project64 v2.4.0-1035-g546ae42 (2019-08-22) or later. 64DD IPL contains fonts and sounds, and is what allows 64DD functions to work as most games relies on it for 64DD region detection.

To play retail japanese games (they appear as grey on the site), you need the Retail 64DD IPL ROM file (click here).
To play development games (they appear as blue on the site), you need the Development 64DD IPL ROM file (click here).
For both of them, go to the Settings, in 64DD tab, and load them accordingly. Or just load the IPL ROMs just like a regular file, it will automatically configure them.

You can load your disk file (*.ndd or *.d64 files) just like any other N64 ROM, via the game list, drag 'n drop, and all that.

When it comes to combo load Cartridge + Disk at the same time, there are now several ways:
- Via Game List: Right click a N64 Game in the list, and select "Load Game with Disk", then select the 64DD Disk file to load alongside it.
- Via Main Menu: Select File, then Open Combo. Select the N64 ROM, then select the 64DD Disk file.
- Via Command Line: Project64.exe --combo [64DD Disk Filepath] [N64 ROM Filepath] There are two save formats, which can be set up in the 64DD tab in the Settings:

Full Disk Copy

A new file is created alongside your 64DD NDD / D64 file, named [filename].ndr / [filename].d6r.
NDR/D6R files are identical to NDD/D64 files on every aspect. It contains the saved data while the NDD/D64 file is unedited. You could rename the NDR/D6R file back to NDD/D64 and it will work properly.
You will notice they are invisible to Project64. Basically upon loading a NDD disk file, it will load the NDR file that's with it first.

Save Area Only

The new default setting for 64DD saves for the latest builds, produces files that will only contain the RAM Area of the disk, as in, the save data.
Therefore unlike the other format where the save file is as big as the disk file, this one can be up to the size of almost 32MB total.
The save file will be named [filename].ram, which is identical to the file format from the Nintendo 64 SDK.

If you want to convert your *.ndr file to a *.ram file, please rename the *.ndr file extension to *.ndd, and then load it as a regular disk.
The resulted RAM file should be compatible with the original *.ndd file. Swapping disks is very easy, however, it has be known: You have to swap when the game tells you that you can.
Simply use "Swap Disk" option under the System menu (or Ctrl+D), and load the disk you want. The previous disk you have used will be saved beforehand.
If Ctrl+D (or any shortcut that has messed up) does not work, close Project64, go to Config folder and delete Project64.sc3. The shortcut list will be reset properly.

You shouldn't need to set anything specific for most of these games anymore as of 2017/12/03.

There are however some problems with GLideN64, such as Mario Artist Polygon Studio's modeling features not working properly.
Mario Artist Paint Studio also has a few issues with transparency if you want to import content in other games.

All 64DD issues would be fixed using angrylion-rdp-plus, at the cost of performance. I would suggest to try it out, as you don't need a powerful PC depending on the game.

Do not forget to UNCHECK HLE Graphics when using angrylion, and likewise, CHECK HLE Graphics when using everything else like GLideN64.

If you want the most performance, you may need to swap plugins DURING emulation to sometimes get things working right .
If you have to do that, you absolutely need to start emulation with GLideN64 and only then you can swap GLideN64 with angrylion and viceversa.

I have included a controller profile inside latest Project64 builds, you can download it here as well:

For games that supports it, I highly recommend also plugging a regular controller alongside the mouse on another port.
The following games natively supports the N64 Mouse:
- Mario Artist Paint Studio
- Mario Artist Talent Studio
- Mario Artist Communication Kit
- Mario Artist Polygon Studio
- Dezaemon 3D (N64)

Setting the N64 Mouse is a bit tricky but doable. I should note that you do not need N64 Mouse to play Mario Artist.
Get to the Controller Plugin's settings and check "N64 Mouse". You will then need to set the mouse controls.
I suggest to use Config 2 for Analog Stick. Change the analog stick controls, and move the mouse accordingly to the direction.
Button A should be Left Click, and Button B should be Right Click. These can be set like usual.

Go to Devices tab. Set the X/Y sensitivity to 30% (it's too sensible at 100%), feel free to find the correct % that you like.
And also set them to Buffered. It's important.

Go to Controller Pak tab. Set the box to "None" and check Raw Data.

And in the Shortcuts tab (upper part), feel free to set (or leave it as is) the Lock/Unlock Mouse shortcut. By default it's TAB.

And there you go. If you want to play again with the N64 controller, uncheck N64 Mouse and set the controls again (and use Config 1 for Analog Stick if you used Config 2 for mouse).