By far the easiest way to use SQLite with electron is with electron-builder.
First, add a postinstall step in your package.json:
"scripts": {
"postinstall": "install-app-deps"
...
}
and then install the necessary dependencies and build:
npm install --save-dev electron-builder
npm install --save sqlite3
npm run postinstall
electron-builder will build the native module for your platform, with the correct name for the Electron binding; and you can then require it in code as normal.