My understanding is that the motherboard controller will handle mapping the virtual memory locations to the physical address of the RAM. As triple-channel memory works, and as most motherboard controllers work, both CPUs will work together to map the lower 4gb of RAM spaced equally along the first three RAM modules (filling up the first three sets of 3gb, working together first), with the last gigabyte spaced among the last three modules.
Without this implementation, there would be no "triple-channel" memory access, thus heavily degrading performance. Furthermore, this is why the implementation of memory is hardware based instead of software, so there should be no problems on your end.
It should be noted that the 4gb limit only exists due to the hard-coded limit of 32-bit memory addresses, but there is no reason for software to allow this limit to be extended. This limit has been selected for license issues, as well as driver incompatibility issues (thanks Josef Grahn). This concept is easier comprehended by understanding that your motherboard, as well as the system RAM, is just another system component. While you may be limited in your working-set RAM, you can actually access the extra 2gb, but not to allow programs to run.
Software exists to allow you to create a RAMdisk out of the RAM which is inaccessable to the operating system, in 32-bit environments. SuperSpeed has a program called RamDisk which will allow you to do this. Another option is the Vsuite Ramdisk software (they both slightly differ - see the features list to see which one meets your needs).
I'm not specifically advertising any software, but those are a few I've come across which allow you to utilize some of the RAM outside of the addressable range of a 32-bit operating system. While it's not nearly as good as having the OS directly access the RAM, having a RAM-based pagefile is much better than a hard-drive based one. If you don't want to use a pagefile, you can also use the extra RAM disk for swap-file intensive programs (e.g. image or video editing).