All four paddles.
I took Elite just because of Halo at the beginning, but then I started using it in every FPS. It was a pain in the ass to get used to it, but after 6 months or so, I finally managed to make a deal with my brain how my fingers should behave.
Bottom left paddle - A
Bottom right paddle - B
Upper Left - Right stick click (running)
Upper Right - Melee (in most shooters or aiming)
That is almost for all popular shooters, but for Gears of War, I got other configuration. Upper paddles are for changing weapons.
Now, I would never jump on something other than just elite. My launch Elite still rocking, after... I don't know how much time has passed honestly. I bought the second one (second hand) for 40 euros a year ago, using it on PS4 with Brook Adapter, of course, for shooters only.
It's funny that I started with two in Halo, it was too complex for me to think and use all four from once. Now it becomes, well I can't imagine playing games without paddles. Of course, I am not using it in simple games such as platformers or driving games for example.
I don't have any pains in the fingers, even from long sessions, it's just so natural for me.