I never raise the espionage slider above 0%.
The spy specialist is really a great deal once you get the courthouse. Getting 4 EPs and 1 beaker is better than running a scientist for 3 beakers, so if I have 2 spare food at that time, I usually run spies in preference to other specialists. Turning 1 commerce into 1 EP in the early game is not a good deal - when it can be 1.25 beakers (with library) or 1.25 gold (with market). So use commerce for either beakers or gold, if possible. Courthouses are pretty much essential to cut maintenance costs early on anyway and the 2 EPs make them a great deal. New cities usually get granary, library, courthouse in quick succession.
Then getting to Constitution fast is a priority. Jails are good for WW reduction and the EPs and especially the +50% is great.
Communism is then another research priority with the Security Agency for another +50%. With these basic buildings in a few cities I get 14 EPs and can run upto 5 spy specialists (another 20 EPs and 5 beakers) and that all has 100% EP bonus. Such a city gives 28 to 88 EPs a turn depending on the amount of food spent running spies. Adding the Security Bureau is expensive in hammers but another 8 EPs is worth double by then so some cities get that as well.
With that set up in 6 or 7 cities (plus a capital with a Great Spy or two) I find I have enough EPs against all the AIs to see their research and counter their espionage attempts by catching spies and making it really expensive. My neighbours get enough EPs to let me see any armies approaching so I get no nasty surprises. If I focus the EPs on one opponent I can look into most of his cities and see what he's built and what he's building... and boy are those AI's dumb
I haven't tried the Great Spy special mission and steal tech idea that NaZdReG is advocating yet. But as I've been the tech leader at Prince and Monarch games I've played so far it wouldn't have been a lot of use anyway

and it's hard to decide which AI deserves that many EPs so my Great Spies have been settled for a slow release of EPs that can be distributed against any AI.
Summary: Don't use commerce to make EPs in the early game. It is a bad deal. Use buildings and spy specialists. Later on when you have several cities with Jails and Security Agencies for a 100% EP bonus perhaps commerce to EPs could be a better proposition, but I've not had to resort to it yet. At that late stage of the game EPs are worth about the same as a beaker or a gold and commerce can be turned into either 2 EPs or 2 beakers or 2 gold in the best cities.