The main reason they are in the amendment portion is because of the debate between the Federalists and anti Federalists ( big structured government vs small localized government) . The anti federalists feared a resurgence of the wrongs brought upon them by the British empire,since during the previous Articles of Confederation, several events had transpired that made some of these power grabs good ideas ( mainly the Whiskey Rebellion and Shay's Rebellion). The anti federalists goal was to craft a new form of Government aimed at individual liberty, rather than broad structure or enacted law.The only way to ensure this liberty would be a written statement of freedoms that the government would need interwoven into it's very core,so that it's entire function rested on maintaining these rights. The Federalist goal meanwhile was to create a Union that served to function as one and as the many seperate voices of the individual states. While individual​ liberty was important to them,reorganizing and restructure in the post AOC mindset was more important,as several similar sentiments (like Shay's) were often common among those displeased with the current government. After all,the main reason for the American Revolution was a failure of Government to listen and react to the people's demands. Any conflict of individual liberty would be held up by those in power based on the will of the people and the harsh memories of being under british rule.

However,the Federalists argued that an explicit statement of such rights was unnecessary,as in their mind,the Constitution was a blueprint for the function and operation of the Government,not (at least at the very core of "x does this when y does that" kind of instruction) a document about the individual. However, several states opposed the Constitution without an explicit statement, and eventually even key Federalist Thomas Jefferson stated "A bill of rights is what the people are entitled to against every government on earth, general or particular, and what no just government should refuse, or rest on inference.".

So it was added in the Amendment portion as more of an "Addition" v.s an "amendium". These rights were never intentionally left out so as to be removed later,but would rather be implicit rather than explicit rights,leaving the Judiciary branch to maintain them.

More sources

• ACLU on the bill of rights
• Key Federalist Paper by Thomas Jefferson explaining views on Government
• Anti federalist paper on foriegn trade as it related to the will of a national government and State government
• Paper explaining Henry's role in the Fed vs Anti Fed debate

There was a pretty spirited debate over the need for an enumerated list of rights for the new nation. Unlike most debates, everyone involved (prominently James Madison on the anti side, and Jefferson on the pro side) was in full agreement that the public had the rights being debated.

The anti side felt that a list of enumerated rights was not necessary. They had crafted a document of limited government. In their minds, since they did not give the federal government the power to regulate speech, religion, or the press for example, there was simply no need to say that the government couldn't do it.

The pro side was not nearly as trusting and felt that it was better to have the rights specifically listed, just in case.

Basically,it was an argument between people who distrusted central government, and this who distrusted it even more.