... which method causes * least stress * on eeprom?

John,

SAVING "wears out" the EEPROM. Method 1 or 2 saves. But you are not going to wear out the EEPROM with occasional changes.
It is only relevant for serial programming when some one uses a procedure that changes frequency maybe every second. Then v1.03 is desirable. I've not checked but many modern EEPROMs specify a minimum of 100,000 writes.

73 Alan G4ZFQ

...method one...
    Serial load;
    05 = 7,000,000
    08 = 7,000,002
    11 = 7,000,004
    etc thru
    26 = 7,000,014
...method two...
    DIP Switch load
    same freqs into same locations
...then...
    Band Select for Clock1 output via
    B2, B1, B0