Actually need to put the code, not in the header preset. Just place it after the menu preset but not within the menu preset because the whole menu preset gets the .sticky class when scrolled.
Something like the below:
.ed-element.preset-menu-any-kind-of-version {…}
.logo-dark{
display:none
}
.sticky{
.logo-light{
display:none}
.logo-dark{
display:initial}
}