From your question we can see that you know how to use some tools, that is good start, but you need to know what you want. I use paper to write down when i run pentest against clients server. I said you, nmap guide book is good stuff to start. After that you need to learn how server works. Install server and try to run exploits against ssh protection, ftp, root etc ...Now i see that you will ask but i need tools for it ? Sure, but, all what you need to do your personal start, open Linux best friend : MR. TERMINAL. Tools will not help you if you don't know how system works.
If i say you that BBox have more then 10 tools to use for information gathering, can you give me their names ? We can say you try Nikto2, but what you will do with, when scanning is over ? If you know how system works, you can move to step 2, if you don't know, tools can't help you. It's not only your problem, it's problem for many people.
How many times you watched WEP cracking tutorial ? 95% of tuts don't say you what to do with KEY you get. Why ? Because pentester knows that people only use their tools to get KEY and show them to friends, they will not use them. Crazy no. Only people with idea to become pentesters will ask, and now, what i need to do ? !.
Hope this will help you !
