Getting Started
To start modifying, you need a modded Switch and a legitimate copy of Splatoon 2. Full guide to modding your Switch can be found here. Do note that following a video guide is not advised, as there is no guarantee on how up-to-date the process described therein is. Also note that, as of now, the Switch 2 is considered unmodifiable.
This guide will start with the assumption that Atmosphere and Hekate has been set up. The Hekate bootloader has a very useful feature in Tools→USB Tools→SD Card which allows you to edit the contents of the SD card while it is still inserted into the Switch by connecting your Switch via USB-C to USB-A (i.e., the Switch Pro cable).
Extraction
One tool you can use to extract the game's data is nxdumptool. Go into user titles menu→[REGIONAL_GAME_ID] Splatoon 2→nca/nca fs dump options→dump base application→Program→RomFS→start nca fs section dump (you will need the game card inserted if the game is not on your system).
You should have a romfs folder within a 0100F8F0000A2000 or 01003BC0000A0000 folder depending on your region. It is recommended to save a copy of this on your computer and leave it uneditted, with all edits being made in a seperate folder.
General Editing
The most general tool for editing Switch games is the Switch Toolbox. It can do most of the functions necessary, but its lack of specialisation means you are better off with more bespoke tools.You should unpack the .pack archives found in the Pack folder (Map.pack, Mush.release.pack, Param.pack, Rumble.pack, Sound.release.pack) into their own folders for easy searching for assets.