If you are referring to the Idaho State MSA program, there is no federal benefit associated with this program - it is only for state income taxes. On the federal return, you would treat this as an ordinary savings account, so you would deduct only those medical expenses that you made from this account (just like you would with any other savings account).
Note that the advantage of the Idaho MSA program is that virtually every resident can get one, unlike the federal HSA and MSA programs, which have noticeable limitations.
Please see the Idaho MSA website for details.