Don't know how much iseful what i'm writing it might be, but Japanese vessels built their pagodas around the already-existing tripods; this means the the three mast legs were left in place and the structure was progressvely added starting from the original platforms. Looking at existing japanese battleships as they changed during the years might be the best way to learn how to do it.
For example look at IJN Hyuga
as she was in 1918 with bare tripod.
Then during the late 20's/early 30's
new platforms were added to the tripod, wich became slowly incorporated in the new structure. Note how the original platforms wre still in their place, altough expanded and sometimes enclosed; the superstructure also began to "grow" inside the aft mast too.
By the late 30's
both the fore and aft tripods had been engulfed by the superstructure, new platforms were added, and many older ones enclosed, often with glassy "greenhouses". Sometimes the top of both mast were slighty cut down i order to improve topweight issues, as much more wight used to sit well above the waterline by that time.
Eventually try to look
here also, beign an AU refit it was concieved by me looking at the Nagato Class as a reference, and not just tracing reference drawings; so it might be another useful example.
The addition of torpedo bulges is something not directly related to the pagodas, but that's a modification that many older ships underwent during the 30's to improve underwater protection; also, torpedo bulges increased the beam and displacement, fixing too some of the issues given by the added topweight. the drawback was a reduction in top speed, sometimes mitigated by replacing coal-fired machinery with newer oil-fired ones; IJN battleships also had the hull lenghtened at the stern in order to mantain speed.