"How does your garden grow" refers to how Mary(the queen of scots)was doing at controlling the country.
"with silver bells..." refers to how Mary was a Catholic and of all the cathedrals that ring bells.
"...and cockle shells" refers to an insult.
"and pretty maids all in a row" refers to 1)How ugly she was compared to other women and 2)How she killed people then: in rows and rows.
