Charles V couldn't even unify Castilian and Aragonese law, much less his disparate Hungarian and Incan subjects. He did his best to manage the Habsburg empire, but in the end he saw it as a fool's errand. That's why he divided the Holy Roman Empire from the rest of his possessions and passed it over to his brother.
While this is a very interesting question, it is difficult to answer in proper context without further asking, "Did Charles V want to unify his various possessions?"
Back to the original question, though, his domains can be broadly categorized geographically.
Spain and its constituent kingdoms: Castille & Leon, Aragon & Catalonia, Navarra.
The Americas, which were all administered under Castille.
County of Burgundy and its areas of control, up to and including the various Low Countries duchies and counties.
Archduchy of Austria.
Kingdom of Naples.
Holy Roman Emperorship.
Did he try to unify some of them? Yes. An example is of the various duchies and countries of the Low Countries, which he forced to be under one union for the purpose of inheritance, through the Pragmatic Sanction of 1549. As a result, all the Seventeen Provinces passed to his son Philip II.
Did he try to unite all of them? No. An example is as /u/TacitusPrime/ said, about Castille and Aragon and Navarre. Castille was where the king's rule was strongest and it produced the largest income. So he deeply cared about controlling it as much as possible. Following the revolt of the Comuneros, he changed it such that in future dealings with the king, the cortes would have to supply money before having their grievances heard. To quote Charles V himself, "Yesterday I asked you for funds; today I want your advice."
To contrast, he left the Aragon cortes alone, because that area was depressed and wasn't considered critical.
Regarding the HRE, your best bet is to read the FAQ here:
http://www.reddit.com/r/AskHistorians/wiki/faq/europe#wiki_the_holy_roman_empire
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