Hey, bud... Sorry I wasn't around yesterday to answer questions. Diving.
Don't feel silly for not knowing how to rig the harness. Someday in the near future you'll be telling someone else how to rig and when they make a mistake, you'll be able to think, "Hey, I remember..."
The bungee should be tied into a circle (think "like an O-ring") using a square knot and melting the ends with a lighter. I also like to melt my knot a little, to make it hard and more likely to stay together. Once you've made the loop, it should be installed WITH the left chest D-ring. That is, one triglide will hold both the left chest D-ring and the bungee loop that you've made. When you're all rigged, your inflator hose will be held down with the bungee loop. I like to put my square knot underneath the webbing (between the webbing and the triglide) for a really smooth appearance.
Alternatively, you can also order the "giant O-ring" from Extreme Exposure. The O-ring isn't as flexible as the bungee, but it's super slick looking, for sure. I like it.
The cutter (and I'm assuming that it came in a pouch made of 2" webbing) should sit just behind your buckle on the left waist strap. When everything's put together, it should sit directly in front of your body, just to the left side of your crotch strap. This will enable you to access the tool with either hand, just in case you become entangled and can only access the tool with one hand or the other. Also, it'll enable you to use the tool ambedextrously when you've already got your hands full with a scooter, light, tool, anchor line, cave reel, SMB, OOA buddy, or whatever.
It should look like this:
Notice the positions of the inner tube. This is used to secure loose straps so that the system gets super-streamlined.
Here's a couple of photos that'll explain what the knife should look like when the rig is fully assembled and you're wearing it.
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No making fun of the dopey-looking diver, now.
My knife is a Scubapro K3 knife, which is rediculously overpriced for what you get - a solid 316 stainless steel knife that's been laser cut from a single piece of stainless steel... With no plastic or handles or anything. I love the knife's simplicity in design, and it's very user-friendly and functional. I think I paid $40-$60 for it.
Most divers I know purchase a pack of stainless steel steak knives and grind the tip down using a Dremel tool or a grinding wheel. Cheap, effective, super-sharp, and of course, you can shape the blade any way you like. I personally think that the K3 looks a lot cooler, though.
The pouch is a simple piece of 2" webbing that's been folded over and sewn to make it. I purchased it from Extreme Exposure, but from what I remember, they don't sell the pouches without the included knife, of which you may or may not be a fan (that's one in the first picture above). I think their Halcyon knives are a bit bulky, although very nicely designed for the hand, and titanium - so it'll stay sharper than my stainless one (304 stainless is much more corrosion-resistant than 420 stainless, but tends to lose it's edge more quickly - titanium doesn't have either of these issues). I'm not crazy about the velcro on the knife pouch - velcro eventually loses it's stick on scuba gear, and can be a pain to operate with gloved hands, particularly if the water's cold. My K3 doesn't move a bit, and is sorta "wedged" into the pouch. I've never seen the need for an additional fastener... But if I did, I'd probably use a piece of inner tube instead of velcro.
By the way... The inner tube is pretty cool stuff. It does break down after a year of sunlight or so, but is easily replaced almost for free. Meanwhile, it's very slick and great-looking. I suspect that you'll need to carry some around with you for your buddies, when they've got a "flying strap." They'll be so impressed.
The coolest thing about the inner tube is that you can cut it to any width you want... Make it wider, and it's a stronger hold... Make it narrower, and it's easier to work with your fingers. I make mine about 1/2" wide for my shoulder straps (for my lights) and about 3/4" wide on my waist strap, to hold down any extra strap.