I enjoy feeding the squirrels I have two that appear to be sick, patches of hair gone and red scabs. What can I do to help them? Will they infect the rest of the squirrels?

It could be a fungal infection or it could be mange. Mange is contagious. It would be better to discontinue feeding the squirrels to make sure that healthy squirrels aren't coming into contact with the sick ones.

If the squirrels have a fungal infection can they survive? Also I have been feeding the squirrels for about two years I'm worried that if I stop feeding them they will go hungry.

Yes, if it is a fungal infection they usually survive, as long as there aren't other health issues going on. Do the squirrels appear to have wrinkled, crusty skin, particularly around the head and face? That would indicate mange rather than a fungal infection. If you discontinue feeding (a good idea if there is mange in the local population), slowly decrease the amount of food you put out over a two week period. This gives the squirrels a chance to find other sources of food. If you keep feeding the squirrels, several small feeding stations spread out on the property are better than one large feeding station that will attract many animals to one area.

The squirrels appear to be getting better. Their faces and underbellies look normal the patches of hair gone is only on their backs and tail. Before their skin appeared cracked and bleeding it seems they are starting to heal. If it is mange how long would it take for them to get better or does it ever go away? These squirrels are very healthy otherwise.

Sounds like it was a skin infection. They wouldn't recover from mange.