"A well regulated militia, being necessary to the security of a free state, the right of the people to keep and bear arms shall not be infringed"
It's there, yes, stating that a militia is necessary to the security of a free state. So what is a militia then? Certainly not what you seem to think. A militia is ALWAYS outside the existing army. A militia is comprised of common citizens who take up arms to defend themselves from tyranny, be they foreign or domestic.
A militia is not a standing or professional army. It's not a draft. How does it relate to the second part? Far from negating it, the right of the citizens to bear arms is absolutely necessary for a militia to form. During the American Revolution, or the Civil War, militias couldn't form without the ability of the common man to take up his own arms.
And why is it worded, "being necessary to the security of a free state"? Because, if the standing army were to come under conrol of a tyrant, as has happened throughout history the ONLY defense for the citizens would be to defend themselves, which is what a militia is.
Take away the right for the common man to arm himself, take away the right of someone to bear arms and a militia can not exist, and the second Amendment would be torn apart.
Actually, it was during the War of 1812 that the militias were found inferior to a federal army. When the war was over, the militias essentially went away as a separate fighting force.
Yes, the citizen was to be armed -- at least, those who fit the definition (males between a certain age). They were to be armed, they had a right to be armed, because they may be needed to secure a free state. It was that right that was protected from infringement by the federal government.