...if we say to keep something 'in mind' it means that we should always consider it/think about it.
So, this would definitely refer to your emotional side - think about your heart.
A similar saying would be 'follow your heart'.
So, in my view, the text
"Identify your genius. Only you can find it. Start with the heart in mind."
means that a person/genius is more than just a brain, your heart/spirit is equally as important.