I know Japan established prefectures in Sakhalin, Korea, and in Taiwan. Does that mean these new prefectures were completely annexed, incorported, and integrated to Japan's core territories? That these new prefectures will stand as equal as the main Japanese prefectures, and are fairly represented to their national parliament?
Also, did they plan on establishing Japanese prefectures in every territory they took? Or did they plan on making some territories mere dependencies or protectorates? If yes, what's the determining factor on whether a territory becomes a prefecture or a protectorate?
Also, were they willing go give Japanese citizenship to the peoples of the lands they annexed?
You're collapsing several different things into one question.
The territories you listed were not part of Japan's expansion in WWII. Taiwan became Japanese territory in 1895, Sakhalin and Korea Became Japanese territory in 1905. Japan also received the former German colonies in Micronesia as part of the settlement of WWI. The international community (League of Nations, etc.) acknowledged those regions as legally under Japanese control, and the original international opposition to Japanese expansion in the 1930s only wanted Japan to go back to its 1920 size, which included all those regions. The allied idea to reduce Japan to pre-1894 size only came about at the Cairo Conference in November of 1943, once the tide of the war had significantly turned against the Japanese empire.
In other words, the question is not "What would the Japanese do if they won the war;" it is "What did the Japanese do in the 50 or so years that they had control in those territories." There have been tomes upon tomes written on Japanese colonial policy, but I'll try to sum up the basics.
The degree to which each territory was incorporated into the main Japanese state varied from place to place. In general, the underlying rhetoric of incorporation was one of civilizational progress - Japan had taken on "the yellow man's burden" and was "civilizing" these "savage" and "backward" regions. On paper, they would be able to join the Japanese empire as equal subjects under the emperor as soon as they had "civilized" enough. In reality, leaders said it would take decades, if not centuries, to "civilize" them, and their status as equal would likely have been in a permanent state of deferral. This rhetoric of a civilizing mission is similar to that employed by many other imperialist powers, but citing racial similarity, Japan was more committed to actually trying to assimilate their colonial subjects.
To do this, the Japanese colonial governments relied on heavy-handed assimilation policies in both Korea and Taiwan, including mandatory use of the Japanese language, and forced adoption of Japanese names in Korea (interestingly, that was just encouraged rather than forced in Taiwan). In the 1940s, as the war situation worsened, The Japanese government did make Koreans and Taiwanese into "citizens," and actually made plans to extend political participation rights in Korea. Korea is probably more notable because of the naisen-ittai, or "Japan and Korea as one" campaign. On the other hand, discrimination was very real, and the extension of rights can easily be interpreted as a desperate concession to keep Korean people's support and authorize the conscription of Koreans as soldiers. T. Fujitani's Race for Empire argues that there are significant parallels between the political experiences of racial minorities (mostly Japanese-American, but some mention of others) in the US in WWII and Koreans in Japan in WWII, and that the racial politics of the US and Japan became more similar as the war progressed.
The expansion after 1930, including the Manchurian incident (1931), The start of the Second Sino-Japanese war (1937), and the Southern advance that started the Pacific War (1941) did not incorporate territory in the same way. See Manchukuo as an early example - rather than annexing the territory, they set up a puppet state and pursued a rhetoric of Asian Cooperation.
During the war, Thailand, Burma, The Philippines and Occupied China were similarly treated as "independent" states (Indonesia and Indochina (Vietnam) were not granted independence, but governed militarily; they weren't "civilized" enough yet). These states and Japan's dependencies were to be united in a cooperative economic bloc, called the Greater East Asian Co-prosperity Sphere. The Co-prosperity sphere was not supposed to expand Japan's territory, but rather to create a stable and autarkic economic sphere--the main goal of all of Japan's post 1930 expansion, driven by the lessons of WWI and the economic hardships of the global depression.
The rhetoric of the Co-prosperity Sphere was that Asia would throw off the yoke of Western Imperialism and have a self sufficient Asia for Asians. Despite the rhetoric of equality, It was clear from the first meeting of the Greater East Asian Conference in 1943 that the Japanese leaders expected to be in control of of the Co-prosperity sphere to ensure that it served their economic goals. While Japan was of course an imperialist power, and undoubtedly extremely brutal aspects, this rhetoric did have a fairly strong appeal, especially in places that had, up until Japanese arrival, been European colonies. Several post-war independence movements had ties to the Japanese.
EDIT: Further reading on assimilation, questions of citizenship, etc:
Mark Caprio, Japanese assimilation Policies in Colonial Korea
Purpose built colonies. While they absolutely intended to reduce the indigenous populations, they had little interest in putting everyone in a big fat grave and then give the land to Japanese citizens. Colonization is always a balance between keeping enough of the locals alive to get work done, but keeping them low and scattered enough that they can't or at least don't organize. Japan had a euphemism for their plan- the Great East Asian Co-Prosperity Sphere- and it kind of resembles what the Soviet Union had for it's post-war Warsaw Pact countries, but where the Union mainly used them as a buffer against Europe, Japan was much more about the extraction of resources.
Japan's land wealth is notoriously poor for resources. Low grade iron, maybe some coal. For them to compete on a global stage they fundamentally needed to rely on economic assistance from foreign countries- particularly oil from the US, along with aluminum and iron- which really bothered some people. It's hard to explain to someone who isn't familiar with Japanese society, but if I had to wing it, Japanese would see it as a threat to their sovereignty that they had to rely on foreigners so much. Japan had a huge chip on their shoulder in the decades leading up to the war because of economic stalling, a massive earthquake that basically burned Tokyo to the ground, and a lack of means to generating wealth. Japanese manufacturing in this era was notorious for being junk. If they couldn't extract anything anyone wanted, and they couldn't make anything for lack of resources and simple experience, they needed to find another way.
If you take a few hours to watch Miyazaki's latest film- The Wind Rises- it actually explains the mindset rather well. Europeans and Americans built wondrous all-metal aircraft. The Japanese used wood and canvas. Europeans and Americans wheeled their test planes out to the field using trucks. The Japanese used cattle. In a world where sovereignty was seen as a product of the economic value a country can produce, for the material poor, manufacturing poor Japan it was extremely frustrating to see that by mere geography they were the backwards lot. They were the ones who starved and couldn't find a steady job. No one wanted to buy Japanese product, but everyone would charge a king's ransom for the Japanese to learn their methods. Japan didn't want to be this- they didn't want to be the next China.