Is there any different between:

1)Nerede otuyor bilmiyorum.
 
2)Nerede oturduğunu bilmiyorum.

3)Nerede oturmuş olduğunu bilmiyorum?

The first two is okay,but the problem is in the third one.

That´s like I don´t know where he had lived?

Biggest problem here is that I don´t know usage of this tense even in English. 

Probably I was sleeping that day at school.  

Don´t sleep, always keep your eyes open. That is what I have learnt so far in my life

I don´t know where he lived.  - this is the past tense

I don´t know where he lives.  - this is the present

Thank´s,I know for lived and lives..
That´s simple,but I rarely use had+ The third column/OR + -ED.
It seems like I wasn´t sleeping that day at school,I remember something.  

I think that "he had lived" is Subjunctive Pluperfect but even I have some problems with it

They called it pluperfect before. I guess it is past perfect now.

Past perfect is used when something had happened before something else happened. Past of the past so to say.

Ahaaa!!!!!! This is the same theory that my Serbian language teacher has told us maybe 2 years ago.. We call it pluskvamperfekat .But I still remember,because I´m young linguist as Abla.

had lived - po srpski bi bilo beše živeo, davno prošlo vreme