This question (as rephrased below) is one that has been and still is discussed in the relevant historical scholarship.

When it comes to the Nazi use of terror and violence as a means of warfare (especially anti-Partisan warfare) and occupation, we dive right into one of the most important discussions surrounding Nazism: situative vs. ideological factors.

Overall, it is important to observe that the Wehrmacht and especially its higher echelons were by the time of the attack on the Soviet Union thoroughly nazified. The war against the Soviets was in their mind not a "normal" war but a war of annihilation. Meaning that civilians as well as the soldiers of the other side were perceived as such an existential thread that extreme violence and terror were the only appropriate measure in dealing with them.

This is apparent when looking at the so-called "Commissar Order" or the Kriegsgerichtsbarkeitserlass (translated as Barbarossa order). Both of these orders issued by the Wehrmacht leadership in the wake of the invasion of the Soviet Union were pretty much criminal in their nature and point to the Wehrmacht and state leadership wanting to encourage the use of violence and murder against the civilian population as well as against POWs. The Commissar Order stated that every politicalcommissar and Jew in the Red Army was to be executed immediately as an agent of Judeo-Bolshevism. The Kriegsgerichtsbarkeitserlass stated that no German soldier was to be persecuted for war crimes committed in the Soviet Union.

These orders coupled with the the internal planning for setting up the occupation of the Soviet Union pretty much shows that the leadership of the state and the armed forces did indeed encourage the use of violence and terror among their troops. In connection with the plans for the occupation, the most famous example is probably the Hunger Plan. Devised by Herbert Backe of the Ministry for the occupied Eastern Territories and General Thomas of the OKW, the plan outlined that several millions of Soviet citizens had to starve in order to feed the Wehrmacht in the USSR.

Another thing that is important for context here are the traditions of the German army itself when it came to anti-Partisan and counter-insurgency warfare. Dating back to the Franco-Prussian war of 1871, the German army was almost notorious for its fear and hard line against Franc-Tireurs and irregular fighters. The German military doctrine was to employ hard reprisals against the civilian population harboring irregular fighters and security threats. This was allowed by the Hague convention and also used in accordance of it during for example WWI but it was a line of thinking that was quickly adapted to Nazi ideology, meaning that it was applied to Jews ("Where there is the Jew, there is the Partisan, and where there is the Partisan, there is the Jew" as the line from Erich von dem Bach-Zelewski ran) and other civilians perceived as a security threat. When for example in Serbia during the uprising of June to December 41 the Nazis ran into huge problems, their solution was to summarily execute 100 people for every dead German soldier and 50 people for every wounded German soldier. In the months between September and December alone the Wehrmacht in Serbia killed around 15.000 people, among them all the male Jews of Serbia.

So, we can say that violence and terror was certainly encouraged from the top down. However, at the same time, the historical record shows that in this atmosphere of Nazi ideology, direct orders to commit such acts of violence and terror were not necessary for the lower levels of the Wehrmacht and the occupation. Klaus Michael Mallmann for example mentions in one of his articles that a Wehrmacht security unit in Poland was shown the movie "Jud Süß" and became so enraged by it and the copious amounts of alcohol they had consumed that they went out and hunted and shot all the Jews of the town they were stationed in. Another example from Serbia in 1941 was when one of the Wehrmacht units stationed there summarily executed Jews from Austria and German who had been stranded in Serbia because they originally wanted to travel to Palestine. These people were in no way connected to the Partisans, yet the Wehrmacht division in question executed them without having been ordered to do so, just because they were Jewish.

The point I am trying to get across here is that while there was an atmosphere of encouraging violence and terror from the top, there are so many examples of low-level bureuacrats or soldiers committing these acts without having been explicitly ordered to do so and on their own initiative that indicate that explicit orders or encouragement weren't even necessary any more at some point.

In short, when burning down a church full of civilians the soldiers didn't need to be ordered to do that because they found themselves in an institutional framework that presented such actions not only as acceptable but as desirable.

Sources:

• Jürgen Förster: "The Wehrmacht and the War of Extermination Against the Soviet Union" pages 494-520 from The Nazi Holocaust Part 3 The "Final Solution": The Implementation of Mass Murder Volume 2 edited by Michael Marrus, Westpoint: Meckler Press, 1989.

• Kay, Alex J. (2011) [2006]. Exploitation, Resettlement, Mass Murder: Political And Economic Planning for German Occupation Policy in the Soviet Union, 1940-1941. New York: Berghahn Books.

• Bartov, Omer (1991). Hitler’s Army: Soldiers, Nazis, and War in the Third Reich. New York: Oxford University Press.

• Walter Manoschek: Serbien ist Judenfrei, München 1993.

• Walter Manoschek: Gehst mit Juden erschießen?, erschienen in Vernichtungskrieg - Verbrechen der Wehrmacht 1941 bis 1944, Zweitausendeins, 1995.

• Klaus Michael Mallmann: "Mensch, ich feiere heut´ meinen tausendsten Genickschuß". Die Sicherheitpolizei and die Shoah in Westgalizien, in: Gerhard Paul (Hrsg.): Die Täter der Shoah, Göttingen 2002.

• Ben Shepherd: Terror in the Balkans, Oxford 2012.

• Dieter Pohl: Die Herrschaft der Wehrmacht. Deutsche Militärbesatzung und einheimische Bevölkerung in der Sowjetunion 1941–1944, München 2008.

Encourage themselves? I am sorry but I do not understand your question.