For example would there have been Chinese trade communities in the Phillipines, Indonesia, and Malaysia and vice versa? Would Chinese and Indian ships have known the location of these places and visited them regularly?
There was plenty of contact, the extensive Chinese population of Malaysia bears testament to this, but Trade was often not in the way we would think of it. the Chinese empire had a general distrust of trade, simply from the rather large can of worms trade opens, as well as the Confucian attitudes towards the profession of trader, which are lets say, not positive.
While trade for money and the exchange of goods did happen, either with the consent of the Asian powers or not, China underwent periods of openness and isolation. The most famous period of openness is perhaps during the reign of the Yongle Emperor, and the expeditions of Zheng He. These and other expeditions involved a unique economic system known as "Tribute Trade" Where China sent and received elaborate gifts on behalf of the state.This sort of conception of tribute could exist since China viewed itself as the only truly existing government in the world, and all other barbarian kingdoms existed in a state of anarchy and were merely client-nations of the so called 1st State. Some of these exchanges were quite not what we would call balanced trade
Source(s): Louise Levathes, When China Ruled the Sea,
A reply to /u/04231993
The trade network connecting the Indian Ocean and the South China Sea was already well established by the time European vessels entered those oceans around the 1480s-1500s. The South China Sea in particular was quite well connected due to its "inland ocean" nature, surrounded by China, Taiwan, Japan, the Philippines islands, Borneo, and Indochina. Some historians have compared this with Fernand Braudel's Mediterranean world.
By the time of the later Ming dynasty, there were already trading routes and networks in the region, however it should be noted that who traded where changed greatly with time. While the Southern Song was happy to allow trade by various entities, Ming rulers tended to want to assert control over their subjects, both for security reasons (they want to keep their nominal subjects under control and subservient to the state; they also want to keep unwanted vessels out; there were turmoil in Japan and Korea leading to piracy) and economic reasons (they want to be able to tax the trade and control what goods come in and out). An outcome of this were the shifting policies of tributary trade and prohibited trade.
There is a fantastic post by /u/_dk that you should read. The trading patterns shifted due to change in policy and change in trade. The tributary trade you may have heard (when you read about Zheng He's storied voyages) was set up both as a means of controlling Chinese subjects and also for controlling the way foreign states had to deal with China. In short, it was intended that the trade be subservient to the Chinese state and be dealt only directly with the state. You can imagine that such a system was unwieldy, inflexible, inefficient, and ultimately insufficient. Foreign states did not always want to, or able to, trade with China under such unequal rules of engagement.
When the Japanese were prohibited from trading directly with China, they set up posts in Taiwan (Formosa) and the Philippines so that Chinese smugglers could meet them there. When Indian ocean traders did not want to pay tribute to China, ports such as Malacca opened up, run by Chinese traders who settled there so that they could claim to no longer be subject to the prohibition.
It was a very complex world that is hard to comprehend unless you appreciate the constant conflict of interest and struggle for control by the various states and actors. As a result, policy arose even when interest may suggest otherwise. The Japanese had silver mines and desired Chinese silk and porcelain, yet the struggle of control and security in China led to periodic bans on trade with the Japanese, in particular when either there is significant rise in piracy by nominally Japanese pirates or when the Japanese state wasn't able to pay the required tribute.
Due to all this, enterprising traders, many of whom are from Fujian, sought alternative means of trading. "Chinese" traders around the Malacca strait supported Portuguese invasion and colonization of Malacca -- even though the Sultanate of Malacca was a vassal of Ming China! These traders were operating outside the control of Ming government and saw their interests more aligned with that of the Portuguese.
Speaking of the Portuguese, as you can imagine when the Europeans came, the situation changed greatly. They were never many in numbers so they had to use the existing resources. The Portuguese controlled the southerly route from China to Malacca, while the Spanish controlled the easterly route from China to Manila. Both powers realized they had to leverage the existing system while on the other hand shaping them to their own interests.
Visible Cities: Canton, Nagasaki, and Batavia & the Coming of the Americas, Leonard Blusse, ISBN-13: 978-0674026148, 2008.
Local and International Trade and Traders in the Straits of Melaka Region: 600-1500, Kenneth R. Hall, Journal of the Economic and Social History of the Orient, Vol. 47, No. 2 (2004), pp. 213-260.
The Formation of Chinese Maritime Networks to Southern Asia, 1200-1450, Tansen Sen, Journal of the Economic and Social History of the Orient, Vol. 49, No. 4, Maritime Diasporas in the Indian Ocean and East and Southeast Asia (960-1775) (2006), pp. 421-453.