A Does だけ replace any particles or do I have to combine every particle with だけ? e.g. だけを、だけが、だけに ...
For the most part, it depends on the formality level of the sentence or rather, the context or situation. In informal speech, we often use 「だけ」 without a particle attached to it. This is true especially with 「を」.
Girls occasionally tell me 「アタシだけ見て!」 instead of 「アタシだけを見て!」.
When they tell me that I am the only man they can depend on, they would say 「レレさんだけが頼{たよ}りなの!」. The only girl who omitted that 「が」 was a foreigner. So I had to correct it for her.
B How does the meaning of a sentence change when I put dake behind a noun or before a verb?
1.だけ in combination with a verb: 私は日本の本をだけ読む。
2.だけ in combination with a noun: 私は日本の本だけを読む。
It is difficult (or actually impossible) to compare the two sentences because native speakers would rarely, if ever, form the first sentence using 「をだけ」. I would not recommend that you use 「をだけ」 even if you learned to use it someplace.
The second sentence is natural for using 「だけを」.
This may not be what you wanted to know, but a more natural way to say this among us native speakers would be:
「私は日本の本しか読まない。」