They're called "two finger brakes" for a reason. Well at least that's what they were called when they were a higher-end item (standard now I think).

Get the Specialized gel gloves (I forget the name, like "Comp" or something like that -- they'll know in the shop). They helped me quite a bit on my folder, which is the first flatbar bike I've had in a long time (no real problems on the roadie). Also, release the DeathGrip(TM). I used to think I didn't do the DG, but I do! Conciously avoiding gripping too hard will eventually turn into a good habit and your problems should go away.