Duct tape! First of all, if you're getting blisters on the bottoms of your toes you might be wearing shoes that are too big or not tying them tight enough. Sounds like you're basically clawing with your toes when you run.
Anyways, wrap duct tape 360 degrees around your toes that are affected. you have to make sure it wraps around far enough to overlap(couple times even), otherwise it'll fall off. Also, do this as long before you actually run as possible. If you really let it set before your feet start sweating it'll stay better. This is the only thing that will stay on when you sweat. Also, the slick outside of the tape means the tape slides/rubs on your sock/shoe and not your skin. I once had really bad blood blisters develop on my big toes from running barefoot on the beach, couldn't even walk, the duct tape allowed me to race a 1500m the next day without pain. It hurts to take off in the end, but it's worth it to run without pain.
I've also heard that the chemicals in duct tape illicit an immune response and actually help your body fight infection and heal faster. Not sure if it's true, but it makes sense.