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The third blessing of the amidah, Atah Kadosh, seems mysterious to me:
You are holy and your name is holy, and the holy ones bless you all day. Blessed are you Hashem, the Holy God.
Is there any particular kavanah that one one should be having while reciting this blessing? We know that God is holy but how is mentioning that a prayer and what significance does it have within the amidah?
The Amidah is divided up into 3 main sections. The first section, consisting of the first three berachot is called shevach (praise). The middle 13 berachot are called bakasha (request). The final 3 berachot are called hoda'ah (thanks).
The beracha of ata kadosh is part of the shevach section (not the bakasha section), so if your definition of the word "prayer" is "request," then the answer to your question, "[H]ow is mentioning that a prayer?" is, "it's not."
I have heard the idea that the reason we put praise before request is because it is improper to approach God and immediately start asking for things. Instead, we start by praising him and then we proceed with our requests. I will attempt to find a source for this idea.
The Ran in his derashos, as well as the Kuzari, both explain the intent of the third blessing as follows:
In the first two blessings, we focus on how Hashem is involved in this world, and in our lives, and does kindness towards us. We describe the middos of Hashem in how He relates to this world. One may incorrectly associate this with being descriptive of Hashem's essence. Therefore, before moving on to the request section of the Shemoneh Esrei, we declare that Hashem is kadosh, entirely separate and beyond our understanding. This is the intent that one should have, understanding that Hashem is, after all our attempts to relate to Him and understand Him, ultimately beyond our understanding.
According to Beurei Hatefilah (see last page of article, esp.) the main focus of the bracha הקל הקדוש is the concept of קבלת עול מלכות שמים (acceptance of the yoke of G-d's kingdom). While this has already been done during the recital of Shema, the article explains that there are 2 type of קבלות. The one in Shema is regarding the past, and the one in Shemoneh Esreh is regarding Mashiach. He claims that the original them of the blessing הקל הקדוש represents the Messianci fervor that existed after the destruction of the 2nd Temple.
