I should probably yield to some of the folks on this board more knowledgable than I, but to hazard a guess, I would say that the Exchange Battalion was merely a temporary unit used to expedite the organization and ultimate reassignment of former prisoners who had been formally exchanged. When I first arrived at Fort Carson, Colorado, in 1970, I was assigned to a "Replacement Company" for 2 or 3 days until they could figure out what to do with me. I imagine it was something like that.
As far as Benjamin and James being missing from the census in 1860, if they were alive, they were likely not heading off to enlist, as general enlistments did not start until 1861 (with the exception of some militia companies getting a jump on things.) Could be they worked somewhere else. Have you check census data for other counties or states and looked for a pair of Smith brothers with those names? Your search would certainly be easier if they were Maeders rather than Smiths!!