waterproofing an XJ what has everybody done to prep for deep water?

I am looking for experience from people involving waterproofing my XJ, like for instance the vent lines for the front and rear axles, i know that on military spec vehicles they run the vent lines back to the air intake box, perhaps also using silicone to seal the distributer? what have you guys done thats worked well and what have you done that hasnt worked well?
TIA

joe