Locomotives and riverine boats are handled by the Transport Pool, at the national level. You can expand this pool to allow more troops to be moved, or at the very least you will want to maintain it, as rolling stocks and locomotives suffer from wear and tear regularly.
But that's not all, as you also have both ocean going ships, and shallow draft river or coastal ships. The Union will have most of these units, unless the Confederate player spend a significant part of his income into a naval strategy ...
