I am going to have gone to bed by the time you come home
Where can I add "already" in this question?
You could add it after "am", but your sentence sounds very unidiomatic.
This would be likelier:
"I will already have gone to bed by the time you get home."
You could place "already" after "am", or before "gone to bed" or after "gone to bed".
I'd probably rephrase to avoid the future perfect:
I'll already be in bed by the time you get home.