Why is the Bill of Rights seperate from the Constitution?

A list of rights had been argued over at the Constitutional Convention, but was not included in the final document because of lack of agreement on its necessity. But it became necessary to enumerate certain rights in order for the constitution to be ratified, and thus it was approved by the first US Congress and ratified by ¾s of the states in 1791.

Much of the arguments were what we hear today. The anti-federalists did not like a strong federal government, and wanted the rights included to protect individuals from the federal government. There were 12 amendments proposed, ten were ratified. Of the other two, one had to do with apportionment of Representatives (never passed), and one had to do with Congressional pay raises, and was passed as the 27th amendment.

The bill of rights are just the first 10 amendments. They are changes to the original constitution.

I second @zenvelo. Also, it’s important to note that “bill of rights” is kind of a confusion, at least in the legislative sense of bill (meaning a law). (It’s a bill, as in a list, see http://www.merriam-webster.com/dictionary/bill%5B4%5D for m-w.com definition). I think the reason for the misnomer is that the English Bill of Rights (more precisely, An Act Declaring the Rights and Liberties of the Subject and Settling the Succession of the Crown.) was legislative, and the federal version is supposedly analogous. Nonetheless, the Bill of Rights in the USA is a series of constitutional amendments that change, or at least clarify, the meaning of text elsewhere in the document.

During that first Constitutional Convention, the Representatives from New York were insisting on a Bill of Rights, but other states were threatening to reject any document that included it.
The solution was New York withdrawing its demand, and pushing for it afterwards, when they would not need 100% agreement.