Setup

1. Install the Goldberg Emulator:
   Open the Endless Space directory by right-clicking Endless Space in Steam -> Properties -> Local files -> Browse local files.
   Create a text file called steam_appid.txt. Inside it, write 208140. Save and exit.
   Rename steam_api.dll to steam_api.dll.valve.
   Download the latest release of the Goldberg Emulator here. Goldberg emu is required to connect two or more instances together.
   Extract it anywhere by right-clicking -> Extract all...
   Copy the steam_api.dll from the Goldberg directory to the Endless Space directory.

(Identical Steam IDs can't find each other in the Join Game screen).

2.1 Launch desired number of instances; make sure to start each instance with different Steam IDs via the Goldberg tab under "Utilities" in the Universal Split Screen tool.

(Launching the game from steam itself created an instance with a single-instance mutant;
launching instances directly from the EndlessSpace.exe does not for some reason.
Not sure if this is normal behavior, or something on my end.)

2.2, Resizing instances:
The "Enable window resizing" option works, but you have to enable it multiple times for each and every adjustment you make.
(Toggle window borders works when it feels like it.)

3.1, Hosting the game:
Select "New Game" from the main menu, and to the right under "Sessions" change "Single only" to either "(X) Multiplayer" option: You will see an error when you do this; ignore it and select "Continue Playing"(This error also shows up when loading multiplayer saves; ignore those also.) After the error displays, return to the main menu.

Repeat the beginning of 3.1 twice. After the third attempt in total, a new error will display; ignore this one also. Loading saves follows this same process.
(What you're looking for is the second error message that has "Steam ID" near the end of the first line.)

To the top left, under "Galaxy", change "Empires" to your desired number of Human and AI players.

Configure other match rules, and you're ready on this end.

3.2, connecting Players:
Select "Join Game" and wait for the host's game to show up.
Select it and then select "Join" on the lower right.

4. Choose/create your factions, confirm match rules, and select "Ready"
   After everyone is ready, the host selects "Start Game".

5. Have fun!

Universal Split Screen options

1. Send normal mouse input (Mouse doesn't work without this)
2. Send normal keyboard input (Above but with keyboard)
3. Send fake window activate messages (Game won't respond to the keyboard without this)
4. Draw mouse (Can't see mouse otherwise)
   Hooks:
5. Filter raw input messages from Windows (Mouse wheel input affects every instance without this)
6. Hook GetCursorPos (Mouse doesn't work without this)
7. Hook SetCursorPos (Mouse disappears and reappears randomly without this)

Results

Other than the awkwardness of 2.2 and 3.1, and that some times when fiddling with 3.1 the mice stop displaying, the game is pretty straight forward to setup, and there are no other major problems I've found during game-play.

I have images of the two errors if you wish to read them.