I perfectly see why you would ask that!

Words like effectivement, certes… are words used to express agreement or objection during a speech (more words like these there : http://www.connectigramme.com/connecteurs.html/concession.htm).

They are often used alone. If it is the case, they just express the person’s view on what the other person just said, when the person has no need to add something to the conversation, beside her (dis)agreement.
For example you might say you like pie during a conversation. If I like pie as well, I can just answer effectivement without further argument, because we agree on this point, pie is good.
However, some can be used in more complex sentences. If I like pie but there are some pies I do not like, I can say certes, mais je n’aime pas la tarte au citron!, which means I agree with you on most points, but lemon pie is a no-go for me.

Pour le coup has more or less the same meaning as certes. I guess you could translate it to “for what it’s worth”.

Further information :

• effectivement is an adverb. It roughly translates to “indeed”.
• it is invariable as it is an adverb. Certes and pour le coup share this property (you can never find or say pour les coups – in this context nonetheless).
• note that some long adverbs in French can bear irony. You can then often find the keyword iron. after an adverb entry in a dictionary. It means it can be used ironically to discredit the person you are talking to. A common example might be when someone answers absolument (“absolutely”) to your argument in a debate when they were clearly against before. But this is not something really important, but I thought you should know.

As for the breath group speech I cannot quite figure out what this expression means, so if you can clarify it I would be happy to edit my answer to cover this point!

As a native French speaker, I’d like to say that these words have a double point. First, they show to the person you’re talking to that you agree with their point of view.

But they also serve as filler words, since I think that a very short sentence as an answer may sound impolite, or your interlocutor may think you do not care about his question.

To my mind, answering to someone’s question without these kind of words may sound like you’re disrespecting him.

– Les résultats du mois sont bons !

– Effectivement, nous avons bien progressé

Sounds way more polite and less conflicting than

– Les résultats du mois sont bons !

– Nous avons bien progressé

"Effectivement" means "indeed", and is used at the beginning of your speech, to say you agree with the people who speaks before you.

• Je vous ai déjà dit que nous ne vendions pas de tomates ici. – Effectivement, j’avais oublié. Je vais prendre des pommes.

Often, it is used to make a concession to one’s argumentary:

• Nous allons acheter la Tour Eiffel. – Mais patron, nous n’avons plus d’agent ! – Nous n’avons effectivement plus d’argent, mais nous avons notre ruse.

In can also be used ironically:

• Les femmes sont nulles en science. – Effectivement, c’est d’ailleurs pour cela que ton école s’appelle "Ecole Marie Curie".

Instead of "effectivement", one can use "en effet" or "certes" that are respectively slightly less formal and a little old-fashioned.
"Effectivement" itself sounds a bit snobbish.

"Pour le coup" is only found in spoken French, and have more a sense of "this time, you are right/wrong", for example:

• Les femmes sont nulles en science. – Effectivement, c’est d’ailleurs pour cela que ton école s’appelle "Ecole Marie Curie". – Pour le coup celle-là était douée, mais ce n’est pas le cas de toutes.

Ma soeur m’appelle tout le temps pour des bêtises, j’en ai marre ! – Pour le coup cette fois c’était quelque chose d’important. – Mais je t’assure que d’habitude c’est vraiment du blabla inutile.

Je n’aime pas cet acteur mais je dois admettre que, pour le coup, il joue son rôle à la perfection.

Concerning the "breath group speech", if you are talking about "gap-fillers" then these words can be used as it.