Probably a 'sticking' intake valve
Atomic-4s are prone to 'sticking valves'; the valve stems get a teeny bit rusted and the friction doesnt let the valve close all the way - the engine fires when the valve is not fully closed; hence, the 'backfire'. Usually the exhaust valves stick when water siphons back into the combustion chamber when there is a pinhole leak in the exhaust system/exhaust manifold. If the problem continues, add some Marvel Mystery Oil to the fuel .... or any "top-oil". this will help coat the valve stems with oil and lessen the valves from sticking. If that 'treatment' doesnt work, remove the spark plugs (and coil wire), spin the engine with the starter and with your thumb in the open spark plug holes determine which cylinder has the 'lowest' compression, then when you shut down the engine for the week, add a few tablespoonsfull of Marvel mystery oil to the suspect cylinder... replace the plugs and with the coil wire off turn the starter to 'spin' the engine without starting. You'll probably have to do this several times until the offending valve stem re-polishes and 'frees up'. To avoid sticky valve stems .... run the hell out of the engine ... and when putting the boat away next winter BE SURE to FOG the engine internals with fogging oil AND put/seal a plastic baggy over the spark arrestor so that wet/damp air cant get into the engine when the boat is stored for long periods !!!!!!!!!!!!! To 'fog' an engine, simply spray the fogging oil into the flame arrestor while the engine is hot and idling until you see heavy smoke coming out the exhaust or the engint stalls .... then seal the flame arrestor with plastic to keep the damp air out during the winter. BTW ... get a copy of Don Moyers "Maintenance and Rebuild Manual for the Atomic-4" www.moyermarine.com expensive but will save you many $$$$$$$$$ in the long run. Hope this helps.