The recommended way to do a SQLite3 query is to use a statement. For a table creation, a query might be fine (and easier) but for an insert, update or select, you should really use a statement, it's really easier and safer as SQLite will escape your parameters according to their type. SQLite will also use less memory than if you created the whole query by yourself. Example:
$db = new SQLite3;
$statement = $db->prepare('SELECT * FROM table WHERE id = :id;');
$result = $statement->execute();
You can also re-use a statement and change its parameters, just do $statement->reset(). Finally don't forget to close a statement when you don't need it anymore as it will free some memory.