A question-word (like what) not immediately followed by a verb forms a noun phrase. "What an amplifier is" is a noun phrase meaning the property which makes an amplifier into an amplifier rather than anything else. A noun phrase can form the object of a sentence.
A question-word (like what) immediately followed by a verb forms a question. "What is an amplifier" is a question. A question cannot be a noun phrase which forms the object of a sentence.
"I don't know what an amplifier is" has a subject (I), a negated main verb (don't know) and an object (what an amplifier is).
"I don't know what is an amplifier" has a subject, a negated main verb, and then a question. In response to a question like "Can you describe an amplifier?" you could say "I don't know: what's an amplifier?" responding to the first question and asking one of your own.
Which behaves slightly differently. "I don't know which is an amplifier" is perfectly grammatical because it's actually an ellipsis — the object of the sentence has been omitted: "I don't know which [piece of equipment] is an amplifier".