The Holy See is a sovereign entity, but is not a nation: it is a diocese that has universal jurisdiction. The territory of any diocese aligns with national/political borders only for practical reasons. If a church building were able to separate its church grounds from its country, it might become a sovereign state, but it would still be a part of its diocese, under the authority of its bishop.
When someone says "the Vatican" they might be talking about either the Holy See or Vatican City.
Meaning of the Holy See Coat of Arms
Since the XIV Century, the two crossed keys have been the official insignia of the Holy See. The gold one, on the right, alludes to the power in the kingdom of the heavens, the silver one, on the left, indicates the spiritual authority of the papacy on earth. The mechanisms are turned up towards the heaven and the grips turned down, in other words into the hands of the Vicar of Christ. The cord with the bows that unites the grips alludes to the bond between the two powers.
Coat fo Arms Information Source:
http://www.vatican.va/news_services/press/documentazione/documents/sp_ss_scv/insigne/sp_ss_scv_stemma-bandiera-sigillo_en.html#Stemma della Santa Sede