Auto-start and Closing Apps

My android device is rooted and its 4.4.2. To control auto-start app, I installed Clean Master and allowed it for root access. I stopped many apps that start automatically. To control start-up app, I installed Boot Manager Xposed. Apart from these I installed other apps also for controlling auto-start and start-up app. However, I have following concerns. 1. In spite of above, I see many apps like browsers, shopping, news, etc; automatically in Running Apps. 2. Whenever I close any apps, I remove them from Recent Apps also. And I keep Recent Apps empty/clean. However, most of time I see closed apps are still in Running Apps. It means those apps not closed completely. I do End Process for all unwanted apps manually every time from Running Apps which is ridicules for me. Till the time, I don’t call/tap any apps, I don’t want see them in Running Apps and once I close any app, I don’t want to see them again in Running Apps. Please let me know to control them.