The smaller ones, the numbered forts would have a single gun level with a lower level for ammunition storage, like most contemporary Victorian era forts. Some of the larger ones had multi-tiered casemates, I presume these were arranged with guns set up to fire rather like the broadsides of an old warship.
The author of the first website suggests that many of the structures atop the casemates were built in the Soviet era and this is probably correct. That said there were definitely AAA and searchlight positions mounted on many of the forts by the time of the Civil War. This was remarked upon by the British during the operations against the Baltic Fleet. Also some of the larger pieces of artillery were mounted in semi open positions, again like much contemporary late Victorian forts elsewhere. Armament ranged up to 11 " pieces with quite a lot of 6" Canet pieces.