Communication between Germany and the Allies was quite possible during the war, and in fact took place quite a lot via intermediaries in neutral Switzerland, Spain and Sweden.

Dönitz succeeded Hitler on 30 April 1945 with the initial intention of continuing to fight, but he quickly realised his position was untenable as news kept arriving of German forces crumbling on all fronts. By 2 May news of the surrender of all German forces in Italy had arrived. As an aside, the surrender in Italy is an example of local commanders (Army General Vietinghoff and SS General Wolff) negotiating their own surrender prior to Hitler’s death. The ceasefire there was signed at Caserta on April 29, just prior to Hitler’s suicide, though did not come into effect until two days later. Anyway, by the time that news reached Dönitz, he had become extremely anxious to reach an accommodation with the Western Allies before the Soviets could gain further control of the German interior. He ordered Admiral Hans-Georg von Friedeburg to go to the British Headquarters at Lüneburg to negotiate a general surrender. This was the delegation you mentioned.

So at 5am on 3 May, von Friedeburg’s delegation arrives by car, under a white flag, at the British front line. They introduce themselves and are conveyed to the Headquarters of British Field Marshal Montgomery. Friedeburg is kept waiting for ages, and when he’s finally admitted, he is a bit indignant because Monty refuses to let him smoke. Anyway, he asks Monty to accept the surrender of the 3 German Armies on the Eastern Front. Monty says no, he can only commit to accepting the surrender of the German forces in the Netherlands, Denmark and northwestern Germany. (The source here is Monty’s own memoirs)

The British are in contact with Eisenhower’s HQ in Rheims and with London. They come up with an Instrument of Surrender which is put to the German delegation. Von Friedeburg returns to Dönitz to relay the terms (it’s about a 2.5 hour drive). Dönitz says okay and starts planning a public broadcast. Von Friedeburg returns to Monty the next day to sign the agreement. Within the following days Dönitz allowed a further surrender of all remaining German forces along the Western Front, this one signed by General Jodl at Eisenhower’s Headquarters.

Now, the orders issued with the surrender gave precise instructions to German commanders on how to capitulate their remaining units and warships. German admirals were instructed to dispatch officers, at least at the rank of Captain, to England, to handover charts and lists of German naval dispositions. These orders were precise, for example:

Party to be dispatched “by air in unescorted aircraft painted white to DREM Airfield 56 02' NORTH 02 48' WEST.” 

“The German Naval Officers who will be dispatched to DOVER and ROSYTH by sea will proceed to positions in latitude 51 19' NORTH longitude 1 43' EAST and latitude 56 47' NORTH longitude 1 13' WEST respectively, where they will be met by British warships and escorted to their destination. The ships or craft in which they travel are to fly a large white flag at the masthead by day and are to illuminate these white flags by night. These ships are to broadcast their positions hourly by W/T on 500 ks. (600 meters) whilst on passage.”

Surrendering in combat was obviously not as orderly, but there was still a clear determination on the part of the Germans to surrender to the right people. For example at the end of the war in Italy, the Germans occupying Trieste were besieged by a significant force of communist partisans from Yugoslavia. The Germans held out until a division of New Zealanders swept into the city, linking up with the partisans to join the siege. Up went the German white flags, and the New Zealanders went in to receive the German surrender (much to the annoyance of the Yugoslavs, who then had to withdraw from the city).