EDIT: This is now outdated. Go HERE.

warning: making this work is a bit cumbersome.

Normal dolphin setup instructions:

Download the correct dolphin version (5.8.7) from here
Download the windows version of the project m sd here (I recommend the google drive mirror)
There are three things you will need from the windows sd download: the files "PMNetplayV4.elf" and "sd.raw" (in User/Wii), and the folder "00010000" (in User/Wii/Title).
Put PMNetplayV4.elf in the same folder as the brawl ISO and launch dolphin 5.8.7. If dolphin can't find your games, set the games directory to where your brawl ISO and PMNetplayV4.elf are. 
In dolphin, right-click the brawl ISO and click "Set as default ISO".
Click "config", go to the "Wii" tab, and check "Insert SD Card". 
Go to the "Paths" tab, and click the "..." button on the bottom to the right of where it says "SD Card Path", then drag the "sd.raw" file into the window that appears, and press "open".
Project M sdv4 should now work in single player. Test this by double clicking on "PMNetplayV4.elf" in dolphin, it should start the game.

Now to make this work in netplay:

The issue seems to be that sdv4 relies on a custom save to work (the 00010000 folder), but when dolphin starts a netplay game, it tries to copy the save to a temporary location and fails. To fix this, we will just manually copy it. 
Note: You will have to do this before every netplay session.

We will turn on dolphin logs to figure out the correct folder to copy the save into.
Turn on dolphin logs by clicking view->show log and view->show log configuration. In log configuration, under verbosity check "Error" , and under log types check "Common".
Now start a netplay game. Once the game launches, make sure nobody clicks "start game" until you're done.
The logs should now show a bunch of errors that look something like this:

Common/FileUtil.cpp:347 E[COMMON]: Copy: failed reading from source: /really/long/path/name/x/y/z/etc --> /var/folders/ab/4w3afp89hwr9g8phre98fhser/T//DolphinWii.xxxxxx/shared2/whatever

The important part is the second path name (that starts with /var/folders). The letters and numbers will be different.
Open the "T" folder in finder by copying everything from "/var" to "T", going to a finder window, pressing "command-shift-G" (or go->go to folder), pasting the filename, and pressing enter. 
Now find the folder called "DolphinWii.xxxxxx" where the x's will be replaced by different letters and numbers for every netplay session. Make sure this folder is the same one from the log messages.
In the DolphinWii.xxxxxx folder there should be a folder called "title". Copy and paste the "00010000" folder from the sdv4 download in the title folder. Make sure you keep the original "00010000" folder since the DolphinWii.xxxxxx folder will be deleted when you close the game.
Now start the game! There shouldn't be any more desyncs. 

A similar process will probably work for linux but I haven't tested it. Let me know if it works or if I missed a step or something. Thanks to https://github.com/FasterMelee/Ishiiruka/pull/4 for describing what the problem was. I hope this helps some people for the like 2 days until 4.1 is released.