The typical syntax is SOV (subject object verb), although this is relatively flexible.
"esse/to be" is a stative verb, however, and does not take an object. It is more common to have SVC (subject verb complement), although again, this is relatively flexible.
Bottom line: Yes, "Philadelphia et Roma urbes sunt" should be accepted as correct. If it is not, please flag it and report "My answer should be accepted."
Nominative vs locative.
Here is a plain-English overview of what the cases are and how they work:
Latin cases, in English
Adjectives must agree in gender, number, and case with the nouns they modify, but they have their own declensions. Sometimes you get lucky and the adjective just happens to follow the same declension as the noun, but that is not a guarantee.