I attempted to find the answer on the FAQ part of AskHistorians, and while there are many good discussions on the different aspects of Slavery (which I recommend reading, especially as it concerns Native Americans) I didn’t find a directly satisfactory answer to your question. So I wanted to go over a couple of things you touched on in your question.

I’m not sure what you mean by “occupied territories”, maybe you are referring either to land within the Confederate States that had been occupied by Union forces by 1862 or the unorganized territories west of the Mississippi not including California, Texas, Kansas, and the Indian Territories. As far as the unorganized territories go, I have little information on slavery within those areas as they were, to my knowledge, sparsely populated by non-native peoples with the exception of Utah. Hopefully someone else can fill that gap in knowledge in this question.

I know that officially slavery in occupied territories was ended in 1862. Was this actually done in that year? Did union soldiers enforce the proclamation?

The end of slavery is a complicated process and indeed pinning down a good definition of when things became “official” is a tall order. It’s important to start with the state of Slavery before the Civil War. The international slave trade was ended in America in 1808 (the earliest date agreed to by those who ratified the Constitution) thus bringing an end to the “official” slave trade, but there appears to be evidence of illegal slave imports to the South through the Civil War. Indeed the Union navy before the start of the war had been dispatching patrols to the coasts of Africa in an attempt to deal with that very problem. However, the navy was small and I assume rather ineffective. So we can check off the international slave trade as officially dead in 1808. Slavery in the Northern states was dealt in a variety of ways. Between the passage of the Fugitive Slave Acts passed both in 1793 and 1850 respectively, many Northern states passed what were called “Personal Liberty Laws” which strike on the always contentious battle between State’s rights and Federal/Congressional laws. However, the federal courts and agents in the North did not have a great deal of success as many in the north abided by the state personal liberty laws. These laws were considered constitutionally shaky as they impinged on the Federal government’s prerogative to regulate interstate commerce, which was part of the legal basis on which Congress passed pro-slavery laws like the Fugitive Slave Act of 1850. Which sought to fine and imprison those who aided fugitive slaves who had run to Northern states.

This issue came to a head not just with the passage of the Fugitive Slave Act of 1850, but also with the Dred Scott decision from the Supreme Court in 1857. That decision was issued by Chief Justice Roger B. Taney in which he stated that no slave “nor their descendants” were acknowledged as “part of the people nor intended to be included in the general words use in the memorable instrument.” Thus Dred Scott had no standing to sue Missouri or the federal government as he was not a citizen who was granted rights. This all serves to show that the nature of slavery as an institution was not simply a matter of legislation or judicial rule at both the state and federal level prior to the war.

Source: “Chief Justice Roger B. Taney Rules against Dred Scott” in The Civil War and Reconstruction: A Documentary Collection ed. William E. Geinapp. New York: W.W. Norton, 2001, 41-42.

Slavery was also an issue for those states seeking to join the union like in the cases of the Missouri Compromise and the Compromise of 1850 which saw the addition of Maine, Missouri, and California to the United States. Also let’s not forget the addition of Texas in 1845, in each case there was significant debate about whether new states were either going to be free or slave states. However, I don’t think I will go into detail about those events unless someone asks a specific question as they are the more well-known events pertaining to slavery in Antebellum America.

Okay, so finally I’ve gotten to the war. Prior to the swearing in of Abraham Lincoln as president but shortly after his election in 1860 several states seceded from the union led by South Carolina. However, despite Southern rhetoric, the fate of slavery upon Lincoln’s election was unclear as he mentioned in the Lincoln-Douglass debates, Lincoln was far from being an ideological abolitionist (much to the chagrin of the more radical part of his party). He instead advocated for continued compromise but took a hard stance on the expansion of slavery. Essentially saying that Slavery could not expand into any more new states.

Source: “Lincoln Douglas Debates” The Civil War and Reconstruction ed. William E. Geinapp, 47-50. (Continue below)

edit: grammar

The abolition of slavery during and after the Civil War is pretty fascinating.

The first step to the abolition of slavery was the Confiscation Act of 1861, which specifically permitted the seizure of property used to support the Confederacy, which included slaves. This was followed by the Act Prohibiting the Return of Slaves of 1862, which prohibited federal troops from returning slaves to their owners. (In a pretty obvious sense, this makes sense. Why potentially support the Confederate war effort by permitting traitors and rebels to get their slaves returned to them?)

This sets the stage for the Emancipation Proclamation of September 22, 1862. Now, the Emancipation Proclamation was a legal workaround, because Lincoln had no power to outlaw the institution of slavery without Congressional authorization, nor could he outlaw the institution of slavery in places where the federal government had regained control. But what he could do is attack the economic base of the Confederacy by freeing the slaves in areas that were in revolt. If you look at the Emancipation Proclamation, the Proclamation does not include the areas that had already been recovered by Federal troops.

Now, as the various Federal offensives gradually cut the Confederacy apart, Federal armies would free the slaves as they advanced. This, caused a massive flight of slaves to the Federal lines.

Everywhere else, including the Union slave states, slavery was actually abolished by the Thirteenth Amendment to the Constitution, passed in 1865.