Eh...key is to have sub assemblies that does not interfer with your masking.
I always glue PE then paint. The idea of gluing painted PE on a model (in which case, the bond is between your paint on the PE and model, not PE and model) just does not appeal to me and feels like the heat contraction/expansion of the season is enough to dislodge such weak bonds. Especially bad for resin/PE because the expansion difference is more pronounced. You also want to bolt the hull to a flag surface in case it warps in the future and dislodges PE.
Masking is not difficult, but just tedious process. Typically you paint the horizonal/deck surfaces first, then mask them, then paint the vertical surfaces (including railings). Cut masking tape into 1-2mm thin strpies of various lengths, trace the outlines of the horizonal surfacesthat you want masked and then fill in the space in the middle with larger pieces of tape.