you're correct in that Ka is just the Keq for a reaction in which an acid loses a proton. genericaly...
HA <--> (H+) + (A-). the Keq = Ka = [H+][A-] / [HA]
now, the "p" of anything is defined as the (-log) of the value. pH is the negative log of the H concentration, pKa is the negative log of the Ka value. now, doing some math and reviewing the properties for adding logs,
-log Ka = -log( [H+][A-] / [HA] )
pKa = -log(H+) - log (A-/HA)
pKa = pH - log (A-/HA)
pKa = pH + log (HA/A-)
the whole protonated/deprotonated stuff comes from working with this equation... when pH = pKa, then log(HA/A-) = 0 and so [HA]/[A-] = 1, that is the protonated and deprotonated forms are equal in concentration. you can remember this equation each time or you can remember the pattern derived from it.... when pH is above pKa the species is mostly deprotonated (A-); when pH is below pKa it's mostly protonated (HA). specifically, the ratio changes by an order of magnitude for each pH point away from pKa... so at 1 pH point above pKa it's 91% A- and 9.1% HA.
hopefully this helps.