I think you should know right off that most of the heavy work with a system isn't really the initial building, it's the hauling of the rocks to fill the media beds. I'm going to suggest for reasons of your climate and the heavy lifting factors that you would be best off keeping media beds to a minimum and using mostly Deep Water Culture. This will add the expense of pond liner and extruded styrofoam for the DWC grow beds, air lines and pump, and net pots. It will likely reduce the number of plumbing fittings you need vs if you used the barrels. You'll have to drill holes for net pots of equivalent to hold the plants. The advantage is that the styrofoam floating on the water will help insulate it (although it will need to be replaced every few years - unlike rocks). The actual beds would be build from the Pallet wood but you might need some 2 x 4 material from the lumber yard. Many set these DWC beds up at ground level but they can be raised as well. DecalsbyJT's thread has some wicking bed builds from pallets that I think would work for this (
http://www.backyardaquaponics.com/forum/viewtopic.php?f=18&t=12933&start=30). His wicking beds are too deep for this so only build them to be about 12 inches deep when full and line them with pond liner. Another version built with plywood is shown on the howling moose gardens thread and in Karens YouTube videos, look for building the trough videos here -
https://www.youtube.com/playlist?list=PLA26ECB8A63FE944F. Probably could do some fusion and get one of your own going. Provided you build them well, you can install H shaped supports or use concrete blocks if you want them off the ground (two posts and a horizontal between them). If you don't have much growing head height build them lower, you'll probably need to bury the sump and pipes enough for the beds to drain in this case. You'll probably be able to skip making a bottom if they are on the ground - I think the pallet wood would just rot. What I would do is put sand in the bottom and just level this, then place the pond liner inside the box on top of the sand. You may run into problems if you have a lot of digging critters around using this method. Termites are a problem for wood in some areas as well.
The movement of the water would be from the Fish Tank to the media beds then to the DWC and finally back to the Sump and then the cycle starts over when the water is pump back up to the fish tank. You might need an additional filter to remove solids before the media beds, some do, some don't - depends on fish loads and I'm not as up on how many fish it takes for good growth in a DWC system (I've seen it but don't remember where

)
As far as layout, you'll need aisles wide enough to move around in but you also need to be able to reach across the grow beds - so figure what works for you (keep in mind it's not the same distance at waist height as at ground level). Since IBC's are close to 4 ft across and you have a good sized but relatively narrow greenhouse, I'd put them at the far end away from the door. Although you didn't say I'm guessing one of the IBC's is to be a fish tank and the other will become a sump and a grow bed since this is what most do. This means that on one side of the greenhouse you will have the IBC grow bed. If makes sense to have it over the sump if possible but you don't want to cover the sump to the point where you can't access the pump or clean it out. Also note that IBC's aren't quite square so it may matter to you, how they are turned against that wall. Turning the grow bed one way and the sump another might be useful. So at this stage you'll need to get a sheet of graph paper (or computer program if you prefer) and draw your greenhouse to scale. Assuming the door is at the middle of your greenhouse on one end, your path should probably be straight down the middle going from this door. This leaves roughly 3 ft to either side depending on what width aisle you need. Can you reach this far across? If not, use narrower grow beds and have other containers stick out from this toward the center aisle to create U shapes where you can step into the middle of the U. 5 gallon buckets from bakeries might be a cheap way to do this. If you want' to connect them to the AP system, you can make your own through the bucket fittings (bulkhead fittings) if you can't find them. I can explain this if you wind up needing it.
You'll need a GFCI electrical outlet to run any pumps or other equipment in the GH.
To give you layout ideas and see how others have done their IBC systems you should take a look through the IBC's of Aquaponics if you haven't already. It's a freebie and you'll see a link at the very top of the BYAP website on the right. Download the PDF version. It tells you one way to cut an IBC but look around because it's been done other ways too.
Ask away if you have questions, someone here knows the answer