Are you referring to the 2007 version?
If so, a thinlight fits perfectly under the outside buckles. Just fold it in half and then into thirds. This makes it really easy to remove for a lunch break, and helps protect the bag. It stays quite snug.
I can't comment on the water resistance, but since there is a top bag, it may be more water-resistant than a top-opening bag, You wouldn't want to have it upside down in the rain, though, due to the way the main bag closes. Also, it uses water resistant zippers, but they are not seam-taped. However, if you use a trash bag, you will use it pointing downwards (since the backpack essentially opens from the lower rear). This may offer some additional protection, too. But you will need a second bag for the top compartment, adding a little complexity. I would think that an inner trash bag with an outer rain cover would give more than enough protection.
I spent about 4 hours once trying a myriad of configurations, and almost returned the backpack. Then I hit on a real winner, and now this is my favorite backpack by far. Here's what I do:
I have found that with this backpack, I prefer to stick the heaviest items at the bottom. By doing it this way it essentially becomes a waist bag with clothing on top, which I find much easier on my shoulders. It also doesn't pull back on my shoulders this way, which I find to be the real cause of shoulder soreness when I backpack. The other trick to this is using vertical stuff sacks, which I will explain below.
I strap my thinlight on the back to make room for a GG sit pad in the main pad pocket. It's more comfortable against my back and adds some structure. I also use it at night for one of my elbows, which always falls off my sleeping pad.
So first goes in the sit pad. Then, in the very bottom of the backpack, I fold up (in 6ths, not rolled) my inflatable pad (BA air core, POE Ether Thermo6 2/3, and Thermarest 3 short all work great). I keep it taught with a velcro strap from REI. This creates a nice rigid rectangular mass, squaring off the bottom of the bag. I find this edge really holds on to my hips; when I use a rounded stuffsack for my sleeping bag (like I do in my other backpacks), it tends to slide of my hips. That was my first "ah hah!" moment with this bag.
On top of the inflatable I add my food, placed flat onto the sleeping pad (i.e. if I were standing with the backpack on, the flat, wide part of the food bag is parallel to the ground). This gives me easy access to food from the zipper, since it is the first thing I see when I begin opening the bag, and it keeps the weight right up against my hips. I'm telling you, the bag feels MUCH lighter with the food there than anywhere else. This was my second "ah-hah" moment.
On top of this goes two vertical stuff sacks, both of them from my GoLite Hex 3 tent and inner nest (~750cc each?). In one goes my Cocoon pants and hooded pullover (perfect fit, not too tight), in the other goes my GoLite Ultra sleeping bag (perfect fit, not too tight). This creates two long parallel 'rods' whose diameter is exactly the thickness of the backpack. This creates several advantages: First, it adds considerable rigidity; if I place the sacks sideways, the bag collapses in the middle. If I use no stuffsacks, everything puffs out of the bag every time I open it. Second, it maintains the rectangular shape of the bag perfectly. Everything else seems to fit better, and it sits real well on my back this way. Third, it places just enough pressure on the food and the top compartment that the rigidity is maintained as the food bag gets smaller. Fourth, it means I can completely unzip the bag and everything stays in place. And by putting the compression tension in the stuff sacks, it removes most of the tension from the zippers. And fifth, it keeps the backpack flatter, thus everything is much closer to my back. The same gear in my Starlight backpack feels heavier and bulkier. Go figure.
With both vertical stuff sack tubes in place, there is now a little depression between them. Into this depression I place my Caladera Cone stove setup (nested inside a Snow Peak 600). This nests perfectly into the gusset of the back panel, and leaves some spare room for any additional items.
Into the top panel I have a 250cc stuff sack with my socks, gloves, hat, and waterproof socks. Next to this I have my emergency kit, my accesories kit, and on top of this my mosquito headnet. This leaves a little room for trail snacks.
The large side mesh pouch contains my groundsheet (GG polycro), stakes, and tent (I can fit a GoLite Hex 3 in there, so long as it is rolled up so a few inches can stick rigidly out the top). The other mesh pockets contain my water bottle and rain jacket. My rain pants go either rolled up next to my sleeping pad or loosely folded on top of the Caldera Cone.
I purchased the hip belts, too. My left hipbelt contains my camera and my Buff Balaclava. The right hipbelt has my GPS, phone, pocket knife and lotions kit (sunscreen, DEET, chapstick, hand sanitizer and Tylenol) all repackaged with BPL bottles.
Lastly, I use a Mountain Laurel Designs bottle pocket to strap a bear canister to my left shoulder strap.
This post got quite a bit longer than I thought it would! Hopefully you can use this template to adapt your gear. But you can see that I can fit a very warm clothing/sleeoing bag kit as well as a fair sized tent into this otherwise small bag, and it all feels so much better on my back than a 'traditional' setup with my Mariposa or Starlite.Overall I am very pleased.