Where are references to daisies? How was she a parallel to the description of her grave when placed in the ordered world of European society?

Your question is a little unclear.  I don't think there are any references to daisies except for the name of the main character, Daisy Miller.  Perhaps you mean to ask if her name has any symbolic meaning?

Well, a daisy is a lovely flower, as Miss Miller is a lovely young woman.

A daisy is a  common flower, so much so that some consider it a weed (see wikipedia link below).   Daisy, and her family, are referred to a number of times as "common," meaning that they lack European sophistication and manners (use the second link below to search the Daisy Miller text for the word "common").  Mrs. Costello, Winterbourne's aunt, considers Daisy and her family to be a weed-like nuisance; in one place, she says that Daisy's family is of  "the sort of Americans that one does one's duty by just ignoring."

Like any flower, a daisy is fragile and vulnerable.  Daisy Miller is portrayed throughout the novel as someone who is in danger of being taken advantage of by some clever, sophisticated European.  In the end, of course, that is exactly what happens.  Giovanelli takes her for a midnight stroll in the Colisseum where she contracts a fever that soon leads to her death.

The only description of Daisy's grave is the following:

A grave was found for her in the little Protestant cemetery, in an angle of the wall of imperial Rome, beneath the cypresses and the thick spring-flowers.

Personally, I wouldn't read all that much into this description.  Perhaps, the author is emphasizing how much Daisy did not fit in with the Roman society around her.  She is buried in a Protestant cemetery in Rome, the capital of Catholicism.  The graveyard is small and overwhelmed by its surroundings, tucked into "an angle of the wall of imperial Rome."  To the end, though, Daisy is lovely--she lies, eternally, "beneath the cypresses and the thick spring-flowers."