We all know that North Vietnam was backed by China and South Vietnam was backed by the US. This is what I know about Vietnam's differences between North and South.
In the North they followed Mahayana Buddhism which was more "liberal" to a degree, while the South followed Hinayana Buddhism which was more "conversative"
for many centuries prior to French colonisation of Vietnam, the North was controlled by the Kingdom of Dai Viet while the South was controlled by the Kingdom of Champa
the Later Li, Tran, and Later Le dynasties in centuries past were centred in the North and were pro-Chinese while the Tay-Son rulers and Nguyen dynasties were based more in the South and preffered international help from countries such as France
I'm not the best with Vietnamese history so please correct me on any of these. French colonisation may have blurred or pretty much wiped out the differences between North and South so all that I just listed may be irrelevant by the time of the Vietnam War. Am I wrong to assume that there are some cultural diferences as well as the political?
It is not inaccurate to say that northern Viet Nam and southern Viet Nam are a bit different culturally. Something to keep in mind is that what became "Viet Nam" did not fully include the Mekong River Delta until 1802. As you point out, Champa and Angkor dominated the southern half of what is now Viet Nam until rather late in the imperial period. Neither of these would be considered "Vietnamese" kingdoms, and Champa and Angkor have rather different cultural histories than Viet Nam, and left a cultural mark on these regions of modern Viet Nam.
I think some of the assumptions you make in your question are a bit off, however. I do not think it is accurate to call the Ly, Tran, and Le dynasties as "pro-Chinese". If what you mean by that is that these dynasties had adopted certain societal norms from China, such as scholar-examinations and the general construction of the imperial system, then fine (though I wouldn't call it pro-Chinese, I would say that these are cultural ideas that the Vietnamese desired to adopt). The Vietnamese considered themselves to be representatives of a "Han" society, however the way Han has been used has changed over time. The meaning behind this usage in this case was that the Vietnamese had adopted the sorts of societal structures that had originated in China, thus were representing this ideal. Confucianism wasn't as wholesale adopted as much as even many Vietnamese like to say, as has been pointed out in scholarly works. Rather, like most relationships between cultures and societies, Viet Nam adopted certain aspects of Confucianism and let go others.
In reality, Viet Nam has a rather complicated relationship with China. Viet Nam was colonized by Chinese dynasties for about 1000 years, with various wars fought between the two in that time. Even after a new independence with the Ngo dynasty, from then on there would be conflicts with various Chinese dynasties. During this time, there were even more frequent conflicts with Champa. During the Le dynasty in particular, Champa was essentially defeated by the Nguyen lords (who later established the Nguyen dynasty). Basically, I do not think you could characterize the "golden age" of Viet Nam as being "pro-Chinese" based simply on some cultural adoptions, nor do I think you could characterize the Vietnamese necessarily as hating China, or at least hating their societal structures.
The Nguyen dynasty was not based in the south. Its capital was the city of Hue, which is right in the middle. Gia Long made this the capital because it was where the Nguyen lords had been living for quite some time. They were the ones who had expanded Viet Nam to its modern extent, and had established their base in Hue. It was probably more or less a feeling of filial piety that led Gia Long to making Hue his capital city. You are correct that Gia Long had asked for aid from France to defeat the Tay Son, however the relationship was strained later as France used this as a justification for colonization and as Minh Mang cracked down on the presence of Christianity. In fact, Minh Mang was rather dedicated in "re-Confucianizing" Viet Nam, so that kind of throws a wrench in the idea that the Nguyen were less keen on Chinese cultural ideas.
Anyways, there definitely are some cultural differences between the three major regions of modern Viet Nam: north, central, and south. It's fairly apparent if you have ever been to the country. The previous rulers of the central and south left a cultural imprint, both with things left behind (such as My Son), and just interactions with the Vietnamese; even the flavors in the foods vary from each of these three regions. To an extent there was a melting pot of cultures. But, I also want to point out that French colonization had an affect on the south. Something to remember is that the French actively colonized a southern portion of Viet Nam that they called Cochinchina. French people actively settled this area and brought with them their culture. Annam and Tonkin were part of the French colonial project (as "protectorates" under the Nguyen dynasty), but they were not the main focal point of French colonization. Cochinchina was controlled directly by France, not via the Nguyen dynasty.
I think the political differences are lesser than you may think. The north and south weren't really separated from each other until 1954 at Geneva. The intention was to have an election between the Democratic Republic of Viet Nam and the Associated State of Viet Nam. The DRVN was based in Ha Noi and the ASVN was based in Sai Gon. The election never happened due to some political maneuvering on the part of the ASVN. It should also be pointed out that the ASVN was established during the First Indochina War (in 1949) in Sai Gon with considerable influence by the French. The DRVN and the ASVN (and later RVN) were separate states but actually claimed sovereignty over the same territory. They weren't exactly separate sovereign geographical countries in the sense that, say, the US and Canada are. The ASVN was a pro-Catholic stronghold (including Ngo Dinh Diem and his family). Of course, Christianity has always been a small minority in Viet Nam, but I think it is notable that Christians were attracted to the ASVN and supported it, and many of the most inmportant figures in ASVN politics were Christians. During the time that Viet Nam was trying to reorganize to prepare for the elections, many of the Christians and others up north moved to the south in order to vote for the ASVN. Likewise, supporters of Ho Chi Minh, socialism, etc. moved north.
If you are interested in the history of Viet Nam, a very good general history is Vietnam, A New History by Christopher Goscha. It's my favorite of these sorts of one-volume histories of Viet Nam.
I think you will also like to look at Print and Power: Confucianism, Communism, and Buddhism in the Making of Modern Vietnam by Shawn Frederick McHale.