The way I run this with my group is as follows: I choose the biggest city in the realm to be the 'capitol' (usually one that has a castle or a temple district) and make it the regular place-of-residence for the ruler and their entourage. This is flexible though - and if the story demands, I will move characters to another city or even to a royal or an army camp in another hex.
But I get your point :) this can certainly be improved by making it clearer in the generated text and maybe throw in a few more royal guards around the chosen royal/holy/etc residence.