Donna, the shallots would have been ready to harvest when the tops first dried up- probably near the end of July. Tormato's ideas for what to do now in your case are what I'd have suggested, too.
The Candy onions also were ready to dig up when the green tops began to yellow to brown and fall over- usually late July-August. Leaving them in the ground until the tops are completely brown is usually risky in climates that have regular rainfall because you want them to dry down completely as quickly as possible to avoid rot. Curing them involves leaving them in a warm, dry place with good airflow until they are nice and dry. If I were you, I'd try to rescue them before all this rain arrives even if it involved a flashlight!
DON'T WASH THEM! Once they're dry, keep them in a dry spot that's not too hot, not too cold. Mine are always pretty good in the basement which goes from about 65 down to about 55 through the winter.
kath