So a few things:
I admire your moxie and wish you the best of luck. But you should probably clarify to your self what you are doing, I don't see a clear goal and there's a bit of confusion in your post.
Second, decoupling is a interesting topic, there are objective Measures of effective implementation. But few projects require that kind of analysis. Rules of thumb:
spread your decoupling into two types bulk and local decoupling. Bulk decoupling is what you are probably asking about, the large 10/20 uf cap. Size/price matters if you are going to manufacture at volume, hence why the beaglebone has 10 uF caps. Err on the side of larger caps when you are doing something where pennies extra don't matter. The other kind of decoupling, local decoupling, take from the reference design, I think I saw 10nf and .1 uf caps on the beaglebone. Get these as close to your pins as possible. Don't skimp on local decoupling, 1 per pin or 1 per group of 2-4 pins minimum.
Arguably, placement and layout of decoupling matters more in most cases than absolute value. Place the caps close to the pins. Always. Keep a high quality ground and power pour accessable to your caps. Bad designs have meandering power rails and ground loops. If you can afford it put a power and gnd plane underneath. If you can't then wide traces, that are the closest to a straight line from your power supply. Go for the widest via that your design can fit, ideally every pin gets its own via or direct power connection. At the power supply side go for multiple parallel vias, like go Overkill.
And finally, choose quality ceramic caps. Don't use electrolytic, tantalums only for bulk, ideally bulk should be ceramic as well.