there is the Osprey book on the general development and tactics, but focussing on the interwar period
http://www.ospreypublishing.com/store/Armored-Trains_9781846032424and the specialized ACW book on railway tactics
http://www.ospreypublishing.com/store/American-Civil-War-Railroad-Tactics_9781846034527with many examples
that should suffice for any kind of wargaming in general, unless You want to dive in deeply on skirmish level historical authenticity, then You will need detailed research.
The downside of railway wargaming this period is that Union and Confederate rail ironclads were very different, so there isn't much of the usual interchangeability and not much capturing (AFAIK), unless You want to keep it basic and use a sandbag armoured flatcar, but this would be a bit boring

If I may offer some personal advice - try to keep the armoured additions/superstructures separate from the basic chassis/model.
I've seen a lot of people here on LAF mangling their basic train models by encasing them in armour plating etc.
Without any doubt every single one became very attractive conversions, but sacrificing the model would have been unnecessary, especially when one can simply unscrew the superstructure and build a new one that doesn't require the civilian version underneath.
You will find following this hint especially useful when You want to game Old West with civilian trains and don't need to buy and paint/convert a new one. Building a tabletop train version is nothing You do on a weekend and pay out of the petty cash...
Building a wooden boxcar with plastic sheet is pretty straightforward even with the sliding doors, and the only difference are the firing slits - the additional armour was from the inside. Building it with removable roof to game inside appears tempting, but You will rarely place based figures in a cramped furnished railcar, apart from an opened door maybe. So whatever You do to the inside only needs to look good from the outside.
I don't think that anyone needs advice how to build a flatcar with plastic sheet. If You go for the improvised sandbags, make sure to fix everything including artillery piece and crew with magnets, since You will probably want to move it around.
Also one final advice - make the rolling stock as heavy as You can - not only will it give You the real feeling, it will stop You from knocking the models over, because anything other than Stephensons Rocket will necessary be larger as anything You know on the tabletop (apart from train models made especially "to fit" 28mm that have the usual scale compression and therefore look meek and unrealistic- but this is my personal oppinion).
Plus, realistic heft will protect You from the unrealistic impression that a 1/56 train travelling at even slow velocity can realistically brake over the length of a normal tabletop

this said, wargaming railway is a challenging attempt beyond the usual artillery range/MG effect "suspension of disbelief" issue, but I find it very interesting and rewarding if one is open to go beyond the usual wargaming conventions
