Our 2006 Monterey's modules are precisely where Larry said his was, and the main one is indeed in the electrical bay under the driver's window.
One note regarding the bay with the 2 lockdown clips, in front of the passenger rear wheelwell: our clips were loose when new, and I wasn't familiar with that bay, though the fellow that did our multi-day walkthrough at BCS in Bend had shown it to us. Then when I had spare time in a campground, I happened to notice one clip hanging down, so I took a closer look and realized they were fully adjustable just by turning the clip's catch in or out on its screw. After snugging them properly, I've had no more problems.
Because that bay doesn't lock, I mounted an easy to reach fire extinguisher in there, and because it has no lamp either, I mounted a small Maglight flashlight in there also by velcroing its nylon slipcase to the plywood frame you'll find in mid-front of the bay. Be careful where you mount stuff though... that frame is to isolate and protect a temperature probe and the Aladdin temp and compass module, so don't put things too close to them.
It's possible your clips have never been adjusted, and the entire bay door isn't sealing across the bottom. You might want to check your clips just in case they're the source of your leak. On the other hand, our electrical bay, where the main Aladdin is, has been on and off soaked all winter, while parked, from water apparently finding its way in from a faulty windshield seal high above it. Hopefully that module missed getting flooded.
Sorry I could only help answer your first question and maybe part of your second.
-Joel