This guide picks up where level creation - exporting ends and assumes you've exported an ASS file.
Introduction
This guide will introduce Tool and demonstrate the basics of how to use it to import your level into the game. Tool is a program run through the command prompt, it does not have a GUI (you cannot double click it).
Tool can also be run through Guerilla and Osoyoos, but it is a foundation skill to know how to run it manually.
Import
Getting your geometry into the game, your ASS file should be in folder similar to this:
(H2EK Install Path)\data\scenarios\multi\example\structure\example.ASS
To start, open your H2EK folder and click on the address bar; type Opening cmd in the H2EK main foldercmd and then press enter. 
This will open the command prompt in our H2EK directory, and allows us to run tool.exe simply by typing Make sure your spelling is perfecttool and then giving it the instructions we want. For our purposes, the command we will use is structure-new-from-ass. 
Type the directory and name of your exported ASS file. Tool always looks to the data folder for importing, so you do not need to include it in the name. Press enter to run the command, during and after the command runs tool will output various information regarding the process, In this example, no errors were reported. Remember to use \ in your file path instead of /
If nothing happens, check the exact spelling of tool structure-new-from-ass and your file path, Tool will do nothing if even a single letter is wrong. If successful Tool will process the geometry, report any errors, and create a new scenario file in the tags folder with a name and folder structure corresponding to the ASS file. If this is the first time importing your level, tool will also assign a default sky and scenario settings, these will not be overwritten on subsequent imports of the same level.
If you are still working on the level at this time, you may leave the command prompt window open so that you can quickly re-import your level as you make changes to the geometry. Press up arrow to bring up the last command you entered.
Most import errors in Halo 2 are the same as Halo 1. This article explains what they are, and how to fix them.
Tool will always report telnet: transport_
You can view a complete list of commands by typing tool and pressing enter. Not all of these commands are functional, and you can also view the complete list here
In-game
Opening a level and playing around in it is simple; Open Sapien, a dialog box will prompt you to browse for a scenario, navigate and select your newly created scenario and open it. 
Sapien will begin loading the level, Since it is essentially running the game to do this it may take a while (However you can save time by clicking and dragging around the Change window position and size to your likingloading map box). When our level has loaded, we will be able to see it in the game window. Arrange the various windows to your liking and press Ctrl + s to save sapien and the scenario. When you close and reopen sapien (Close Sapien using Alt + F4 to avoid potential corruption), the windows will remain as you left them. 
Navigate in the game window by selecting it, then holding the middle mouse button and using the WASD keys, use R to ascend and F to descend. Press shift to cycle through camera speeds and hold Ctrl for speed boost
Taking a stroll
Next, we will spawn in and walk around the level as a player, in the The first entry will represent initial player equipment, the second for respawn equipmentHierarchy view window select and expand the Game Data folder, select Starting profiles and click New instance. 
In the properties palette, you can customize the starting equipment for Players Set the player gear as you desire
In the Forgetting these will make levels unplayableHierarchy view, select and expand Player starting points, Select the none folder and right click in the game window to place a starting point, when playing this level this is where the first player will spawn, add another for player 2. 
Next, select the Spawn the player where you clickPlayer simulation folder, then in the game window right click to place the player character and then press Tab to switch to player mode. You can now traverse the level as the player character, Press Tab again to leave player simulation. 
Make sure to save your level every time you make changes you want to keep, using Ctrl + S.
Your next step after you finalize your geometry and have everything imported should be lightmapping.
Acknowledgements
Thanks to the following individuals for their research or contributions to this topic:
- odchylanie_uderzenia (Markdown conversion/editing and publishing)
- quag (Writing this guide)