The following sentences confuse me a lot:

Is maith atá a fhios agam é! - I have good knowledge of it
Is maith go bhfuil a fhíos agam é! - It is good that I know it

In the second sentence, "go bhfuil" is an indirect relative so the phrase before and after are not directly related. I presume in this case that means that nothing within the second phrase is good rather the whole phrase itself. "Is maith go bhfuil" basically means "It is good that which is expressed in the phrase after me"

However, in the second sentence you are pointing in to the phrase after "atá" and saying that something there is good. I'm presuming that since the noun "knowledge" (fios) comes first, it is the knowledge that is good.

What if you wanted to say, "I am good for having knowledge of it"?

How would you say the following in Irish:

The good man has knowledge of it.
The man is good for having knowledge of it.
It is the good man that has knowledge of it.
The man has good knowledge of it.
It is the bad man that has good knowledge of it.
The bad man has good knowledge of it.
The good man is bad for having little knowledge of it.

No, it is no indirect relative clause here. It is just a subject clause.
"That" is a relative pronoun and a conjunction in English. In case of a relative pronoun in can be substituted by "which", but not in the second case (my English is too bad, but I think that is the best way to differentiate them). Here it can't be substituted by "which". So, it is not a relative clause.
"Go" in Standard Irish (and Connacht/Ulster) is only a conjunction, not a relative particle.

To make things more complicated: In Munster, "go" is used instead of the indirect relative particle ("a" with eclipsis in Standard Irish). But even in Munster not all "go"s are indirect relatives. Most of the time it is a simple conjunction in a subject or object clause.

But your presumption is right: Yes, the whole phrase is subject to "is maith".



Not really ...
It is a case of tréisiú, i.e. topicalisation of "maith"
The normal word order would be:
Tá a fhios agam go maith é. = I know it well, I have good knowledge of it.
"tá a fhios ag ..." ("tá's ag") is treated as a normal verb, so it can have adverbs like "go maith". You'd rather don't say "Tá a fhios maith agam é".
If you want to put the focus on "go maith" you put it first in the sentence - which now is introduced by the copula.
Is maith ... (You don't use "Is go maith ..." usually, because it is no adverb anymore here but an adjective)
The rest of the sentence follows as a direct relative clause:
... atá a fhios agam é.



Don't know. (I struggle with the English meaning ...)



Tá a fhios ag an bhfear maith é.
?
Is ag an bhfear maith atá a fhios é
Tá a fhios ag an bhfear maith go maith é. or Is maith atá a fhios ag an bhfear maith é.
Is ag an drochfhear atá a fhios go maith é.
Tá a fhios ag an drochfhear go maith é.
?