It would easier to discuss if I had a pic to look at.
I have seen quilting in flowers and animals to enhance the design. But I don't like the method of just randomly quilting over them, like an all over stipple pattern. I think it distracts from the applique, but thats just me!
Look back at some of the gorgeous quilts the pros have posted on here, many of them have applique.
And I think the suggestion to ask the maker is a good one.