I have been slightly confused about when to use the suffixes mi/mu/misin/musun and so on. I have looked at a lesson on this site and it seems you only use the suffixes when the answer is yes or no such as

Sen yoruldun mu?

Is this correct? If this is the case then I now understand how to ask questions!

Not necessarily, The answer could be yes or no.

" mI, mi , mu , mü  "  are  question suffix  that are used to make questions.

Sen mi  ? ---> Is that you ? 

Bu kalem mi  --> Is this pen ?

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With verbs this ending are used seperately. And the personal marking is attached onto it. 

Geliyor musun? ---> Are you coming?

Geliyor   mu  [question suffix] + sun [suffix for person "you]  ? 

Geliyor mu ?  ---> Is he/she coming ?

Geliyor muyum ? ---> Am I coming ?

Geliyor musunuz ? ---> Are you [plural] coming ? 

Geliyorlar mı ? ---> Are they coming ? ---> This one is exception as personal ending [lar] is attached onto word.

Yes, "Sen yoruldun mu?" is correct way  to ask " Are you tired" ? [ did you get tired ?]

Although it is in past tense form "du" , it asks present state " Are you tired" ?

in other words, we are asking if the person is tired at the moment. 

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"yorulmak" in fact means  = to get tired 

If the question was referring to past time ; 

Were you tired yesterday ? "  then  ---> " Dün yoruldun mu ? "

I thought ´yorgun´ is tired. 

Yes, yorgun is tired.  

But "yorulmak" is to get tired . 

Yoruldum be usta

Ben de çok yoruldum. 

Yes.

Were you tired yesterday? "  then  ---> " Dün yorgun mu idin? "

Did you get tired yesterday? "  then  ---> " Dün yoruldun mu ? "

thank you everyone for your help.

My main question is when do you use the suffixes mi/mu/misin/musun and so on. It seems to be mainly if the answer is going to be yes or no though someone answered saying that doesn´t always apply.

I understand if you say geliyor musun? are you coming?

and i understand nerede gidiyorsun? Where are you going to? you wouldn´t say nerede gidiyor musun would you?

I have learnt enough turkish and turkish sentences I need to know when you add the suffixes but I don´t always understand the logic!!

No you wouldn´t.

The easiest way to start to think about it is that you do not need the end question marker in this sentence as you have it in the first word.. NEREDE gidiyorsun... WHERE are you going.

Sentences with neden, niye, ne zaman, (why when what which etc) do not have MU/MI/ MUSUN etc etc (question markers )added at the end

nerede gidiyor musun?

It may be meaningful in some context.

(For example; x and y talking on the phone)

x: ...´a gidiyorum

y: öyle mi?

x: nerede gidiyorum tahmin bile edemezsin.

y: nerede gidiyor musun?

x: evet bir balonda ...´a doğru gidiyorum.

thank you insallah. Thats makes it clearer for me.

Balonda gitmek de mümkündür, ama seyahatin çok uzun süremez...ancak balonun bir köşesinden diğer köşesine gidebilirsin.

Eğer niyetin balonu bir vasıta olarak kullanıp, mesela A şehrinden B şehrine, gittiğini anlatmaksa iş değişir; "balonda" gidiyorum değil, "Balon ile gidiyorum" demek gerekir.

It may be possible in my Turkish. We speak different languages, I guess.

We can try the same thing in English as well.

I ask their opinions from English speakers here:

I´m going by balloon. (sounds weird to me)
I´m going in a hot air balloon.
I´m going on a balloon. (could be right, but I wouldn´t use it..)

I´m going by taxi.
I´m going in a taxi.
I´m going on a taxi. (wrong unless you mean you´re on the roof)

I´m going by submarine.
I´m going in a submarine.
I´m going on a submarine. (this one could be okay, just like "on a boat," or "on a plane," but I wouldn´t use it)

I dont understand now, why it´s nereDE gidiyorsun and not nereYE.
I thought in Turkish it must be like that,which is unlike in my and English language.

"nerede gidiyorsun" and "nereye gidiyorsun" don´t have same meaning.

"nereye gidiyorsun" means "where do you go?"

For "nerede" lets imagine a dialogue like this: 

A: Üniversiteye gidiyorum. 

B: Nerede gidiyorsun?

A: Ankara´da.

In this dialogue "nerede" has a meaning like "in which city"

Sagol gokuyum.