structures like the wells are getting waterlogged stairs

Had this issue too, especially with mvs:well/small_well, which usually causes flooding in the surrounding area

if you're using certain mods from yung or integrated dungeons etc. you can use their waterlogging processor and apply them to the processor list of the problematic structures

e.g.

{
  "processors": [
    {
      "processor_type": "integrated_api:waterlogging_fix_processor"
    }
  ]
}

if you're using certain mods from yung or integrated dungeons etc. you can use their waterlogging processor and apply them to the processor list of the problematic structures

e.g.

{
  "processors": [
    {
      "processor_type": "integrated_api:waterlogging_fix_processor"
    }
  ]
}

Could you expand on how to do this?