Answering your second question first.

Ancient Empires like Rome and Persia may look similar on a map through being big blobs but they were possibly at opposite ends of the administration spectrum. Rome operated on tax and all laws and regulation came from a centralised government in the senate. The administration was then decentralised and passed out to various provincial governors and prefects, chosen by the senate. Though initially it would be quite diverse in later periods of the Roman Empire it would be pretty homogeneous throughout the empire as the Romans liked it if you were Roman and were also good at absorbing local customs.

Persia relied on many client kings who all declared loyalty to The King of Kings and provided tribute and armies for him. These kings could declare their own laws and raise the tribute any way they liked. It was also very culturally diverse. Egypt would be much different to Western Anatolia and again to the Persian heartland. This diversity worked as each region was ruled by a king of their own culture.

EDIT: (I'm no expert on the various Persian empires and, after a little research, I appear to be wrong on the matter.)

The client king system existed in Ancient Persia before the founding of the Achaemenid empire by Cyrus the Great. He established a number of Satraps who were governors over provinces. So this appears to be similar to the later Roman model of provincial rule.

Moving on to Charlemagne. Charlemagne was the creator of the system of land division that survived throughout the medieval ages and on to the 17th/18th centuries. He divided his land into hundreds of counties, each with a count/comte and a bishop who he would appoint. This system was copied in other parts of Europe. In some places he would put a few counts under the rule of a trusted Duke and in the border regions, Saxony and Northern Spain mostly, he created larger defensive divisions called marches. The ruler of the march was placed under a very loyal subking, usually a relative of the Carolingian king.

You can read up on Charles V and his empire from my profile page. He largely ruled through regents, and had to deal with each domain's rules and parliaments individually. Indeed, he travelled often in an era where itinerant courts were the norm.

As far as movements of armies, he had to first raise them. I have written on this subject and you can read some of my posts from my profile page. When he first took possession of Spain he demanded large sums of money and disrespected the parliaments and nobles. This led to a critical revolt of the Comuneros. In the HRE he lacked soldiers until 1525 when he defeated Francis I decisively and was able to march his crack troops from Italy to Germany. This meant he was largely on the defensive against the Schmalkaldic League until 1525.

He attempted to unify the succession of the Low Countries in order to secure his son Philip II's ascendancy there. He also took possession of Milan to secure lines of communication.

His person and his empire is a very complex subject. Feel free to ask follow up questions!

To make a modern metaphor, image 2 scenarios. In one, U/Starbuckrogers is elected to the governor in 5 different states. In another, you're elected the governor of one state and conquer 4 more. In the latter case, even if those states are physically separated, you are imposing some unity on them from above, they're all aware that they got conquered by you and you're a central authority for all of them. Now imagine being elected governor of 5 separate states at once. None of those states much cares about the others. They all want your attention and none is going to be willing to subordinate itself to the needs of the others. They each have their own local laws, legislatures, etc, and if you tried to homogenize them you'd get enormous push back.

That's what happened to Charles V. The Hapsburg basically won the inheritence lottery and, over the course of a century or two, went from German dukes on the edge of Europe to running an personal union that spanned the continent. But none of those parts really thought of of themselves as part of a coherent entity. They thought of themselves as spanish or nepolitan or genoese who just happened to have hapsburg king, not parts of a great Hapsburg empire, and generally resented it when their soldiers or tax dollars were sent abroad.