The Czech region of Czechoslovakia (Bohemia and Moravia) developed much differently than the Slovak region prior to their integration in 1918. The Czech lands had been the center of industrialization for the Hapsburg empire, while Slovakia had been cut off from the Czech lands through a process known as "Magyarization" in which the Hungarians (the Magyars) attempted to erase Slovak culture (as well as other cultures within the Hungarian region of the Austro-Hungarian Empire). When Czechoslovakia formed in 1918, the Czech lands inherited 4/5 of the industrial capabilities of Austria-Hungary. One might have expected rapid growth in the Slovak region once the Slovaks were reunited with their Czech cousins in Czechoslovakia, but in fact Prague (the Czechoslovak capital) implemented policy that kept the Slovakia a junior partner in the Czecho-Slovak relationship. For example, of the 100+ generals of the Czechoslovak army on the eve of Hitler's occupation of Prague, only one was Slovak. Many Slovaks resented Czech domination of Czechoslovakia, which became important to Hitler's overall Czechoslovak strategy describe below, but the main point here is that Bohemia and Moravia were valuable prizes for Hitler because of their industrial might while Slovakia lagged far behind.
Of course, Hitler could not occupy Bohemia and Moravia while ignoring Slovakia. Instead, he worked with Jozef Tiso of the Slovak People's Party, a right-wing party demanding more autonomy for Slovakia, to create a new nation to act as an ally of Germany and to provide Germany with a pretext for the invasion of Czechoslovakia. Hitler called Tiso to Berlin and told him that if he did not assist in the plan, then Germany would allow Hungary and Poland, which had already seized areas of Slovakia in the previous months, to completely annex the small nation. Tiso eventually yielded, and although it was not easy to convince his party to make such a declaration, the Slovak parliament finally did issue an official request on March 14 (crafted by Berlin) that Germany move into the Czech lands in order to protect the sovereignty of a newly-declared Slovak state. The following day, Hitler ordered his military to occupy Prague and the Czech lands.
Given that Slovakia was an afterthought in his conquest of Bohemia and Moravia, the creation of a puppet state in Slovakia proved a deft move by Hitler. He created a military ally (and Slovakia did commit divisions to Hitler's upcoming war), invented a pretext for the invasion of Czechoslovakia (however obvious it was), and avoided committing resources to a pointless occupation of Slovakia (until after the Slovak Uprising of 1944).
Chad Bryant, Prague in Black: Nazi Rule and Czech Nationalism, Harvard University Press, 2009.
Stanislav Kirschbaum, A History of Slovakia: The Struggle for Survival, second edition, Palgrave Macmillan, 2005 (original edition 1995).