The following should work for you and enable you to choose when to use the direct Ethernet link. Try this:
1) Manually assign IPs to the Ethernet interfaces of the two connected Macs. Use IPs that are in a different subnet than the subnet being used on your wireless network. FOr example if your Airport network is using 192.168.X.X then use 10.0.0.1 and 10.0.0.2 for the wired Ethernet interfaces with a 255.255.255.0 mask.
2) On both Macs order the Ethernet interfaces after the Airport interfaces in Network preferences pane.
3) On the computer assigned the 10.0.0.1 IP, use a text editor to edit the "/etc/hosts" file and add an entry like "10.0.0.2 Mac2Ethernet". Choose any hostname you want in the place of Mac2Ethernet.
4) On the computer assigned the 10.0.0.2 IP, use a text editor to edit the "/etc/hosts" file and add an entry like "10.0.0.1 Mac1Ethernet". Choose any hostname you want in the place of Mac1Ethernet.
5) Then, test things out by opening terminal on one Mac and trying a "traceroute Mac#Ethernet". It should only have one hop, directly to the other named Mac". Try it in reverse from the other mac as well. You may also want to test a traceroute to an Internet destination and make sure that it does NOT route through the other Mac but uses the Airport network instead.
6) Then, when you want to transfer a file from one Mac to the other simply use the alternate hostname Mac1Ethernet or Mac2Ethernet for those Macs and the traffic will only use the direct connected Ethernet interfaces. For example, on Mac1Ethernet, type command-K in Finder to get to "Connect to Server" dialog, then use afp://Mac2Ethernet to connect to the other Mac.
I'll leave the testing of this specific configuration to you but can tell you that I do currently use something very similar to connect my iMac to a TimeCapsule next to it using directly connected Ethernet. This allows very fast wired backups for the iMac even though it uses a different Airport network for all other home networking and Internet.