I am slightly confused by what you mean by "multi-layered metaphors." Do you refer to extended metaphors? These are defines as metaphors that are carried on through a series of lines of poetry, developing the comparison rather than just establishing one point of comparison and not developing it further. If this is what you are referring to, then Dickinson does use extended metaphors a lot in her work. Perhaps the most famous example is "'Hope' is the thing with feathers--" which compares hope to a bird that perches in the soul which never stops singing and also never asks for anything in return:
"Hope" is the thing with feathers--
That perches in the soul--
And sings the tune without the words--
And never stops--at all--
Note how the extended metaphor is established in the first line of this poem and then extended and developed throughout the poem, building on the first comparison.
The poem above represents one of Dickinson's most straightforward extended metaphors, but she displays much more sophisticated use of metaphors in poems such as "The Soul has Bandaged moments--" where the soul is compared to a variety of different objects. Dickinson is incredible subtle in her use of metaphors, so this is a subject worthy of much analysis.