OK here we go.
With a ram air setup you are talking about an actual scoop mounted somewhere on the front of the vehicle.
The scoop or funnel feeds a tube that leads directly to the airbox or cold air chamber (like a FIPK). At speed this setup will actually creat a slight amount of boost of forced induction. Of course you can also use a carefully placed hood scoop to grab your air but again water will flow right in unless baffles or expansion chambers are used.
On Mustangs often the scoop is mounted below the front faring which is only a couple of inches from the ground. So yes if you hit a deep enough puddle your gonna get your filter wet, worst case actually get some water past the element and into the intake.
With a Cold Air feed system it's basically the same idea:
Some sort of feed tube is used to direct air from behind the grill to the airbox or cold air chamber. The difference with this setup is there may not be room for a funnel or scoop to grab as much air. What I have on my truck is simple. remove the stock (crappy, leaking, and restrictive) cold air feed tube. This will also have a vacuum actuated valve in it that controls flow to the hot air return hose (connected to pass side exhaust manifold) that can be removed. I cut the opening in my radiator support (about 1.5"x3" stock) open to 4" diameter. This is located just below the battery tray on early model Explorer's and on all BII's. I then used a piece of 4" dryer hose (thick black rubber kind) and a 4" PVC to floor toilet flange behind the new hole. This routes below the battery tray and over to where the airbox used to be. It actually fed my airbox at one time, which also had to be modified to accept the 4" tube.
I now have a 7" K&N cone mounted to the end of my MAS where the airbox used to be. This feed tube simply fills the cold air chamber I built (Similar to FIPK). If any water does happen to splash up behind the grill, up the tube and into the cold air chamber, it will simply drain out.
There is not enough pressure or suction to force the water through the K&N cone.
This is not a ram air setup because it never generates enough pressure to create boost. It is just a great way to ensure that your intake is not sucking up hot underhood air, thus increasing power, or actually keeping it from being decreased.
Now the third option is called Cowl induction.
this usually requires a rearward facing scoop or buldged hood. There is a low pressure zone of swirling air right at the base of your windshield. This is whay the factory put holes here to suck up fresh air for your heater system. This air is always cool and always flowing. Making it ideal for your intake. Re-location of extensive plumbing is required on our engines to get that cool air to the intake filter.
Regardless of which setup you use anytime you drop the temp of the incoming air you gain HP. So even after spending time and $$$$ on your cold air fed intake there are other things to consider. Dropping the overall underhood tempature is a must when you are looking to squeeze every single possible ponie from your powerplant. Heat insulation can be used on some stuff, header wrap can help, but a good cooling system and is the most important. With a 180 thermostat, a 4 core aluminum radiator (4.0L HO cooling package) , the supercooling mechanical fan and clutch (11 blades I think) and synthetic oil my 93 OHV 4.0L runs right at 190 no matter what. She will get up to 198 when towing but drops right back down to 185-190. Of course keep in mind my BII weighs 4200#, not 5500 like a base Explorer.
My JBA headers increase the underhood temps a little bit so I made sure to install heat hose guards and heat insulation wherever possible (fuel lines, heater box, etc..)
My intake setup cost me about $50.
$35 for a K&N 7" cone
I adapted it to the MAS meter with a gasket and bolts
$15 for misc hardware and feed tube.
This is no 20 HP adder like say exhaust could be, but for $50 its a real nice way to finish off the rest of the intake and exhaust mods.