From my understanding, flags and emblems played a huge role. As far as signaling a flag holder when to raise their flag to let their troops know to get ready, not sure about that. Likely they would just use something as simple as a runner who would go up and down the lines repeating the generals orders.

I've talked about communication in battles with specific reference to feudal Japan here, which I'll quote below.

Though not an extensive explanation, Stephen Turnbull's The Samurai Sourcebook states that Japanese armies were definitely capable of issuing orders throughout the battle, either with drums, shells (used as horns), or flags, and to a lesser extent, gongs and bells. There would be systems set up before battle to explain what certain rhythms/calls/flags meant, as well as sequences and combinations that were understandable only by the same side - it wouldn't do well if your flag read "Flank their left side" in plain text for the enemy to read.

Turnbull also goes on to say that messengers on horseback were also used to relay information from the general or daimyo to the individual commanders, or samurai. Understand that, whilst there were individual 'sub'-commanders that commanded a 'unit', a lot of the time the leader would be moving forward an entire line of attack/defense, rather than a small group of soldiers. This proved especially true during the Sengoku period, whereby larger armies composed primarily of peasant ashigaru made it a necessity to communicate to a wide group of footsoldiers.Messages might have been relayed half by writing, half by word, and decoys were possible as well, to prevent the leaking of information if the messenger was captured and tortured.

Similarly, during battle, a command hierarchy existed, as did regulations and general rules, and as was expected, authority was followed. If it were a daimyo who called for the army to assemble, they would be the commander, if it were a loyal retainer, they would command, and so on. The commander-in-charge would, before hand, also set up a plan, possibly outlining certain features (e.g. forests, mountain slopes) - an example of this would be the fourth battle of Kawanakajima, between the two daimyo Uesugi Kenshin and Takeda Shingen - one of Takeda's generals formulated the plan of driving Uesugi's army down from a hill on to a plain, where Takeda's army would be waiting in ambush.

Essentially, horns, banners (or rather flags), and drums. There were also messengers that could be sent from the central command unit to other parts of the army and their commanders.