There are three problems:
The FAQ (https://www.graphviz.org/faq/#FaqDotWithNodeCoords) tells us how to achieve node and edge placement. Label placement is done using newlines. The code was hand-written.
digraph ontop {
big [label="B\n\n\n\n" pos="2,2" shape=square height=1]
little [label="A" pos="2,2" shape=square height=.4]
big:e -> little:e
}
Command line:
neato -n -Tpng ontop.dot >ontop.png