Bootstrap gets used at different places. It is already configured by default by the BootstrapAsset and is a dependency for other pre-defined assets. But you can override the default location.
Assuming you have the same file structure in web_assets
as it can be found in 'vendor/bower-asset/bootstrap/dist' (contains folder css, fonts and js) you can add the following to your components configuration:
use yii\bootstrap\BootstrapAsset;
...
'components' => [
...
'assetManager' => [
'bundles' => [
BootstrapAsset::class => [
'sourcePath' => null,
'baseUrl' => '@web/web_assets',
],
]
],
...
],
@web
points to the web folder where the index.php and your web_assets
directory file should exist as well. sourcePath
gets set to null since baseUrl wouldn't be evaluated.
Further information about configuring the used bundles can be found at AssetManager::$bundles or in the guide.
Similar question is here.