These are not stupid questions at all.
Have you considered getting an EM100? That would give you a little more debugging.
A post card is about the single most useful thing to have in the early going, so you should probably get that before you go much further.
Beep is a lot harder than it used to be. While simple code may work on Linux, there's a lot more going on under the hood, because the simple beep can be driven by a very complex audio pipeline. Beep may not be a good place to start.
Here's a slightly bigger question: does it have to be an x86? Could it be ARM?
Because here's a true story. I'm answering questions from some security researchers who *were* working on a haswell chromebook (Acer C720). Last week they realized that Intel was not going to make the blobs available for the memory startup (MRC) and the ME for haswell chromebooks. Those blobs are available for the sandy and ivybridge chromebooks, but nothing that came after. Result: all the researcher's work is moving to the Samsung ARM Chromeook because the ARM vendors tend to be a lot more helpful (save for AMD, nowadays; there are lots of unanswered questions there). I'm sad about that because Acer C720 is a great laptop and haswell is a great chipset, but what can you do?
Note that the new Acer 13 is an ARM Tegra system that runs coreboot.
So, just to be sure: it has to be an Atom? It's a much harder road than an ARM nowadays.
ron