Thee first two possibilities mean that the speaker is confident that the statement "today is the day that you have been waiting for" is correct.
Certainly, today's the day you have been waiting for.
Today's the day you have been waiting for, certainly.
The next sentences emphasises today, ie this is a very important day for you.
Today's certainly the day you have been waiting for.
The next sentence emphasises the waiting, suggesting that (somehow) you have
put a lot of effort or enthusiasm into the waiting.
Today's the day you certainly have been waiting for.
The next is called a split infinitive: putting the adverb between the auxiliary verbs (have and been) and the participle (waiting). Some people think that split infinitives are wrong. Again, the emphasis is on the waiting, but the meaning of certainly changes- see the next example.
Today's the day you have been certainly waiting for.
The final possibility transfers the certainty from the speaker to the listener, who has been, for example, waiting for the results of an exam,
confident that they have done well. You could in fact substitute confidently to make it absolutely clear.
Today's the day you have been waiting certainly for.
I am not quite sure what you mean by the second example, but it looks like an "Is a split infinitive OK?" question: have a look at the link I gave you earlier.