1. "Where are Tom and Jim in the morning?" 2. "Where were Tom and Jim in the morning?"
Both sentences are correct. The meanings are different.
Sentence 1. can mean "Where are Tom and Jim every morning?" or "Where are Tom and Jim every Wednesday in the morning?"
Sentence 2. can mean, "It is now 3:00 pm. Where were Tom and Jim this morning?"
3. "Where are Tom and Jim usually in the morning?" 4. "Where are Tom and Jim in the morning, usually?"
When you change the regular word order, you emphasize the word that is our of order. In sentence 4., the word “usually” is out of word and is emphasized. If you need more examples, please feel free to ask.
Hirashin, I have a tricky one for you. Do these sentences have the same meaning?
I know the difference of them. Happily in #5 modifies the verb "left". So it is calld a "word-modifying adverb (語修飾副詞)". The one in #6, on the other hand, modifies the whole sentence. So it is called a "sentence-modifying adverb (文修飾副詞)".