Why did the emancipation proclamation not apply to the entire US?

Answer 1

Under the Constitution, Lincoln did not have the general authority (nor did Congress) to declare an end to slavery in the states of the Union. But in the exercise of his "war powers" as Commander-in-Chief, he could take a wide variety of steps against those at war against the nation. This included confiscating property or freeing slaves being used to support the Confederacy in its fight against the Union. But for areas not in rebellion (esp. the border states that had not rebelled) he had no authority to touch their slaves. (The Proclamation actually included a specific list of the states and parts of states in rebellion on January 1, 1863, the date the proclamation went into effect.)

Note that Lincoln, and Congress, did take other Constitutional steps to free slaves not covered by the Proclamation - beginning in April 1862 with the freeing of all slaves in Washington D.C. (the one place Congress had authority to legislate on such matters), and proposing a Constitutional amendment (the 13th), which finally passed Congress in January 1865 and was ratified by December of that year.

Answer 2

He did, but not everyone complied willingly