I use more than just two fingers whenever possible. More fingers or my whole hand is even better.
Some times I feed the fabric through with my fingers, then I will switch to using my seam ripper. For me it is keeping them in the same position for too long, overusing the same muscles.
Stop very often, massage my hands, warm them up and rest them higher than my heart (for the swelling), use larger ergonomic tools.
I have tried snug fitting gloves too.. they do help to take the strain off of my hands. Mine are a nylon, breathable and fingerless, found them at a sporting goods store :D:D:D