To maintain order , and protect the Czechs - which is why they didn't offically annex the land into the Reich, but instead turned the Czech parts of Czechoslovakia into 'The Protectorate of Bohemia and Moravia' ( under German 'supervisory administration' of course )

After Sudetenland , Poland and Hungry also took parts of Czechoslovakia, and what was left of Czechoslovakia started to fall apart - the Slovak and Ukranian parts of the country declared themselves to be autonomous states within Czechoslovakia and the central goverment lacked the power to refuse.

The Hungarians were not satisified with the amount of land they were given at the First Vienna Award ( a treaty a month after Sudetenland, which was meant to stabilise the situation ) , and continued sending small numbers of troops onto Slovak lands - with the goal of ultimately taking most of the Slovak and Ukranian parts of Czechoslovakia for themselves ( with some encouragement from Hitler - who in the end let them take the Ukranian part )

Czechoslovakia wasn't strong enough to stand up to Hungrey's threats , so Slovakia declared full independence in exchange for a protection treaty with Germany.

Hitler then used the declaration of independence as an excuse to move into the remaining Czech lands on the ( not totally unfair ) basis that Czechoslovakia as a state had failed.