To say an idea is embedded in you seems reasonable - I would take it to mean that the idea is fully understood, has become part of your thinking, and isn't likely to be forgotten until it is fully realised.
To say that you are embedded in the idea sounds odd - how could you be within an idea? The idea might involve you, but there isn't really a process of putting you within an idea that could be described as 'embedding'. It would of course depend on the context you had created around it.
If you are trying to say that you are fully committed to the idea and its realisation, the idiomatic expression would be "I am invested in that idea".