The best way I've found is just a single spy per army/general. They don't have to be trained up in any significant way.

Personally, I usually designate a single city in the interior (so it is non-coastal, and thus lower trade/profitability) as my spy city where I build up the brothel line, and produce spies when for my own protection, and occasionally to keep taps on that city I'm going to attack in a few turns. Just don't put a governor where you building the spies.

As for assassins, I don't think they add any true protection, but I could be mistake. I rarely use them.

Oh, and Thieves Guilds help spies, no assassins.