Method of methods

What is the right approach to use set of rich selection of methods and tools? I don't dare to say that I know it but I think that I have some ideas.

1. We have to have something which allows us to have a good overview about the utterly complex environment we are sitting in.
2. Prioritize; we must be able to decide what to tackle first. 
3. Dig deep: we have to go to the root cause and solve it profoundly.
4. Set up/improve procedures.
5. Establish controls and monitoring and keep the running.
6. Start over again.

This is very similar what is suggested in the Theory of Constraints, albeit not the same. Anyway TOC is a very important element of my idea of managing the mess.
So what are the tools and methods to the steps above:

1. Overview:  I haven't found any real good method yet. The reason is I think that it's really complicated. UML can be one tool, TOC reality trees an other example. What I really prefer to draw a pictures about the systems (if I can).You will need some (e.g. one for infrastructure and other for BO systems and a third for major processes). These pictures must be detailed enough to cover every subsystems or sub processes but clear enough that anybody can understand them easily.
2. Prioritize: may favourite is TOC
3. Digging deep: Lean Six Sigma.
4. For process improvement Lean Six Sigma is the best I know. It also works for process design but I have no experience with that. The only thing I have used is the good old flowchart.
5. I have good experience with ISO 27001, but it doesn't cover everything and seems to be a bottom up approach. Balanced Scorecards is top down, I have found it a bit difficult. LSS also has process control elements, but I think it is not strong or definitive enough. What should be used in IT by all means is the good old cost controlling. However what I'm working on a long time is a service catalogue with automatic monitoring. Not easy but even defining it made a change.