잘 지내셨어요?
잘 지냈어요?
Both correct and different in honorifics.
All verbs and adjectives can be converted into an honorific form by adding the infix -시- (-si-) or -으시- (-eusi-) after the stem and before the ending.
지내셨어요 is an honorific expression of 지냈어요
지내셨어요 is composed of 지내(다)+시+었+어요
지냈어요 is composed of 지내(다)+었+어요
지내셨어요 used when talking with someone superior in status, for example older relative, a stranger of roughly equal or greater age, an employer, a teacher, a customer, or the like.
지냈어요 used when talking with someone not superior in status, for example younger stranger, a student, an employee or the like.
Refer to
http://en.wikipedia.org/wiki/Korean_honorifics