The organization and hierarchy of the Empire were complicated to say the least. It wasn't a Kingdom in the true meaning of the word, like France or England for example. It had some republican characteristics, but it wasn't a republic either.

In the Empire, there were thousands of settlements: villages, towns, convents, monasteries and hundreds of additional places of worship. All these communities were linked by the imperial constitution, which bound them in a series of hierarchies, often with overlapping jurisdictions.

Basically, the Emperor was the superior lord over lesser authorities, bound by the chains of vassalage. Those lords who were immediately under the Emperor's jurisdiction (Reichsunmittelbar) ruler over fiefs (Reichslehen) given to them by the Emperor. The Reichslehen were generally composed of lesser holdings, like villages and towns. And on the other hand, the ecclesiastical lords, who had a very close relationship with the Emperor, considered themselves a separate collective within the Empire - the 'imperial church', or Reichskirche. However, a person holding one type of authority wasn't barred from owning another, so a lord of an imperial fief could also hold other land that would bind him in vassalage to one of his peers. In its entirety, the Empire was made up of around 310 fiefs and the rights to rule over them were most often acquired by inheritance and were held by the 50-60.000 noble families in the Empire. Most of these territorial nobles (Landadel), which possessed lesser rights and were subjects of the imperial lords.

By 1521, all the political subjects within the Empire were organized into three groups. The most senior were the electors - seven lord who held the exclusive right to vote in Imperial elections. Three electors (the Archbishoprics of Mainz, Trier and Cologne) were ecclesiastical, while the other four (Bohemia, Brandenburg, Saxony, and the Palatinate) were secular holdings.

The other fiefs fell into one of two types. 50 spiritual fiefs, and 33 lay fiefs. The lords who ruled over them were called princes, even though their actual titles could range from Landgrave to Duke. The lay fiefs could be transferred through inheritance or purchase, but both required the Emperor's approval. The rulers of ecclesiastical fiefs, on the other hand, were picked by commissions established by the Reichskirche, and were subjected to Papal approval. The second group of fiefs, numbering around 220, were smaller still - they consisted of only a few thousand subjects ruled over by a count or prelate, who lacked a princely status. The Reichsritter - Barons and landed knights, were even smaller, and held 1.500 other fiefs.

There were also cities - communities who fell outside of lordly jurisdiction. There were 80 'free and imperial cities' within the Empire, with tens of thousands of citizens. Their size gave them considerable influence and ensured the mayors of the imperial cities a very close relationship with the Emperor, which guaranteed their sovereignty and preserved them from being incorporated into the neighboring principalities.

The Imperial Constitution dictated that the Emperor was overlord and sovereign, holding considerable power that he derived from his title rather than his fiefs. His prerogatives were left vague on purpose, so as not to limit the Emperor's 'holy, universal' pretensions. However, the need to deal with pressing problems forced the definition of the relationship between the Empire and his vassals.

The lords of note secured representation in the Reichstag, or imperial diet, and were recognized as imperial Estates, which gave them precedence over those who weren't. The Reichstag was basically a proto-Parliament, which embodied the principle of representation through the Emperor's obligation to consult with his noteworthy subjects on matters of state. But this is the Holy Roman Empire we're talking about, it has to be more complicated.

The consultations with the Reichstag took place in three separate colleges - the Elector's college, the cities' college and the princely college. Each college took a decision by a majority vote, but beforehand, every representative spoke in turn according to a strict order of precedence. After all three colleges had separately reached a decision, they consulted each other in pairs. Electors talking to princes and mayors, and so on. After this entire process was finished, the decision was presented to the Emperor as a recommendation, which he could accept or reject. Even though the Emperor didn't have to consult the Reichstag, it was a useful tool for testing public opinion and further proving imperial legitimacy. Though cumbersome, Emperors called the Reichstag into session fairly often, especially when it came to matters about the entirety of the Empire.

TL;DR: The Emperor was sovereign which delegated control to lesser lords who ruled overhundreds of holdings with separate and overlapping authorities, which sometimes banded in a type of proto-Parliament to decide on matters of state.

Source: Peter H. Wilson: The Thirty Years' War - Europe's Tragedy

PS: Even though my source is a book about the Thirty Years' War, it includes a huge preface about the political organization in the Empire.

Edit: Oh, and if this doesn't answer your question and you want a more precise answer, feel free to ask a follow-up question.