He should not be given any special treatment. He should not be addressed as anything other than Private Manning. He should not be allowed to wear a wig or any clothing other than mens prison wear. He should be made to maintain men's grooming standards according to military regulations. There should not be any alterations to his appearance or gender. He enlisted as a male and he should serve his entire 35 years in prison as a male.
A prisoner is denied certain rights and have their freedoms confiscated after being convicted of a crime. Manning is a prisoner. Also, people who join the military are aware that the laws that govern soldiers are different from civilian law, and many aspects of the Bill of Rights do not apply to soldiers, or apply in such a manner as to make them irrelevant (example, the criteria for "reasonable" search and seizure in the military is "any and all circumstances", which justifies inspections and etc). Manning was a soldier, who upon being discharged was thrown into prison. Therefore, the only real question is "should the government pay for Manning's sex change?" And the answer would be no.