So, I know exactly how to do this when the IDE isn't in the way; I just edit the linker ld file and I have a nice day.
I want to reserve a word at a specific location for special treatment, either by defining a special segment or by defining the start of memory to be at 0x2000 0004 instead of 0x2000 0000. (It's for clean bootloader to application communication, BTW).
How do I do that in AtmelStudio?