Get out paper and pencil. Storyboard out that you're seeing in your mind's eye, including movements, morphs, color changes, 2D/3D, etc. Then write back with a detailed description of what you want to do.
There's no such thing as a standard "merge logos" effect, so nobody can give you an adequate answer.
Sr. Promotion Producer
KCRG-TV (ABC) Cedar Rapids, IA