'In three hours, I don't know what should I do' incorrect grammar, unless there is a special reason within the style but it does not apply here
'In three hours, I don't know what I should do'
is correct but the meaning is
"
After three hours
pass, I don't know what I should do."
It sounds very strange to place "in (or for) three hours" at the beginning. It sounds better at the end of the sentence.
I don't know what I should do for three hours.
Should is not the best choice. Three hours is long time. The speaker
cannot decide about his action or if there is an appropriate action at all.
Should is used better if you have several options but you can't make a choice, or if you know you probably have an obligation but cannot recognize it at the moment.
I don't know what I'm going to do for three hours.
I don't know what I'm going to do for the next three hours.is probably the most precise.