AGP Adapters/slots are keyed by voltage, which also translates to which AGP version is installed.
The AGP Graphics Aperture is a somewhat misleading name. The Grahpics Aperture is not the window that you can access the video memory on the display adapter with. Instead the Aperture is an amount of memory which the graphics card can use to access system memory when it runs short of memory for rendering. So, if the aperture is set to 512MB, for example, you are dedicating that chunk of address space for the video card to use. You are also keeping that memory from your computer!. Most BIOSes work OK with the default value, or 1/2 video memory, or must about 128MB (since most video cards these days are huge).
With a 32 bit processor (4 GB address space), this very reason is why the system will "lose" installed memory -- it depends on how large the video card memory is, plus how much memory is allocated to the AGP Aperture. This problem is "fixed" on 64bit CPUs running in 32 bit mode, and on Intel Xeon CPUs with >32 address bits. The kernel can map the display memory above real memory.
AGP Memory modes:
NEC 2010 x LCD Display