To use SQLite in Ionic in an organized way, the best approach is to encapsulate database operations in an Angular service.

Installing the plugin

cordova plugin add cordova-sqlite-storage

Creating the service

angular.module('app')
.factory('DatabaseService', function($cordovaSQLite, $q) {
  var db;

  return {
    init: function() {
      db = $cordovaSQLite.openDB({ name: 'app.db', location: 'default' });
    },

    query: function(sql, params) {
      var deferred = $q.defer();
      $cordovaSQLite.execute(db, sql, params)
        .then(function(result) {
          deferred.resolve(result);
        }, function(error) {
          deferred.reject(error);
        });
      return deferred.promise;
    }
  };
});

Call DatabaseService.init() inside $ionicPlatform.ready() and use DatabaseService.query() in any controller to execute SQL queries.