I won't try to talk you into using Linux for this adventure, but I will try to talk you into using a simpler ARM platform. You should try something like a TI Launchpad with a Cortex-M class processor; not only will the TRM for the platform be much more reasonably-sized, but the M architecture is actually much nicer for bare-metal programming, especially if you are using C! It's also a much better platform for real-time work; sometimes the pipelining and other tricks that the A-series CPUs use to increase throughput comes at a cost of non-deterministic execution times, which are the enemy of real-time programming with hard deadlines.
In either case, from TI you'll want the platform's Technical Reference Manual and Datasheet. The TRM generally has in-depth descriptions of the registers and programming models of all the peripherals that users are expected to use, while the Datasheet will generally have an overview of the functionality provided, the memory mapping of the register banks for the peripherals, and pin-out information for interfacing with the chip. On top of that, you'll want several manuals from ARM. You'll want the ARMv7 Architecture Reference Manual (there's one version for A and R series, and another for M series-- BBB has an A series core) as well as the more specific Cortex A Series Programming Guide (or the M Programming Guide if you go with an M-class CPU instead of the BBB) and the Cortex A8 (or Cortex M3/M4) Technical Reference Manual, which together tell you everything you might want to know about the CPU itself, at least outside of the minor modifications and implementation choices TI made when putting it in the BBB's SoC. There are various other useful documents in ARM's library; a handy one for low-level stuff is "Procedure Call Standard for the ARM Architecture" which shows you what assembly instructions constitute a procedure call that can be used to call into compiled libraries.
For a look at what bare metal programming on an M-series (such as the $14 Tiva C Launchpad from TI) board looks like, here are some slides from a guy's tutorial presentation along with a handout pdf that's very informative:
http://www.bravegnu.org/blog/gnu-eprog-slides.htmlI was able to get that toolchain working and run a couple of basic programs in an emulated (via qemu) ARM M3 platform. Really, a microcontroller is the biggest thing you'd *really* want to write all the code for as a hobbyist. Digging through TRM details and RAM datasheets to figure out the correct timing parameters to program into your SDRAM controller is really not a lot of fun, and you'll never have the time to get a fraction of the BBB's peripherals up and running without taking advantage of a LOT of pre-written code. Microcontrollers, on the other hand, are all about bare-metal code and just the functionality you need for the job you're doing. A Tiva Launchpad would be a great board to experiment with bare metal programming, basic motor control and sensor reading, etc. It'd make a nice little robot brain, or even just a nice little platform to experiment with developing a bare-bones RTOS. If you skim through the A-series and M-series references, I think you'll agree you'd much rather be doing bare-metal programming on the latter.