It was very, very difficult particularly given the countries in between Charles V's territories - notably France - were often hostile to the Habsburgs. The difficulty of administering all the disparate territories contributed to Charles V's stress and decision to abdicate and divide his lands between his son and brother.

In regard to the Low Countries there was a route called the "Spanish Road" which passed through Lorraine, the Free County, Savoy, and parts of Switzerland and was used to move forces overland between today's Belgium, Italy, and Austria. Believe it or not a well-drilled army could move relatively quickly using this route.

Sea transport was also used, and was faster, but as one might imagine obstacles to this would emerge depending on who the Habsburgs were at war with at the time.

The Duke of Alba famously used the Spanish Road while en route to the Low Countries to suppress the Dutch Revolt. Generally, the Spanish would leave a military garrison (the army of Flanders) to quell unrest in the southern Netherlands and fight the Dutch rebels during the 80 Years' War. Organized into the tercios, this army was multi-ethnic in character with soldiers from Spain, Germany, and elsewhere and owed personal loyalty to the dynasty.

After the War of the Spanish Succession, the southern Netherlands passed to the junior branch of the family (the Austrians) who appointed governors to the region (usually German nobles). As you mentioned, the centralization efforts of Joseph II led to the Brabant Revolution which is the start of Belgian nationalism. Ultimately, the southern Netherlands were annexed by the French Republic during the War of the First Coalition, and later were ceded to the Kingdom of the Netherlands after the Vienna Congress.