Well, the answer to this question is complicated by the fact that while in terms of international law such a thing as a "protectorate" exists (as a partly sovereign territory with its foreign policy and defense policy handled by another power according to an international legal contract), the specific form of the Protectorate of Bohemia and Moravia and the construct of the General Government were things the Nazis pretty much made up and ran with and that weren't really based on existing, recognized institutions of international law. In the end, both Protectorate of Bohemia and Moravia and General Government were fancy names made up for the illegal annexation of Czech territory and the occupation of Polish territory. As such, Allied nations never recognized these acts and the status of these territories (as they never recognized the illegal annexation of various Polish territories into the Reich). So, from an international perspective, both Czechoslovakia and Poland continued to exist under Nazi occupation with their legal and proper governments remaining in exile in London.

The Germans, naturally, took a different view. But to them, the Protectorate and the General Government had different statuses. The Protectorate of Bohemia and Moravia was, according to Nazi legal view, a territory that was part of the Reich, having been annexed in 1938/39 respectively (founded with the Munich agreement and the annexation of the Sudeten territories, completed with the occupation of the Czech Republic and with Slovakia becoming a satellite state under a nominally independent government).

The exact status of the Protectorate was spelled out in the Führer decree of March 16,1938. According to this decree, the Protectorate was part of the German Reich but autonomous and self-administering, with the "Head of the autonomous administration" enjoying the protection and honor rights of a head of state, the post and traffic administration falling to the Reich, the Reich being able to pass laws for the Protectorate but the current laws still remaining in effect as long as they don't contradict Reich law. Also, the Reich Protector had the power to counter any law or other provision as well as introduce new laws and provisions and generally, do whatever he pleases with regards to the administration and bureaucracy of the Protectorate. So generally, while the German government tried to present the Protectorate of Bohemia and Moravia in line with some of the international precedents of what a protectorate was, most historians and legal scholars agree that despite a limited nominally autonomous administration existing under German command because of the far-reaching powers of the Reich Protector and the Reich itself with regard to the Protectorate of Bohemia and Moravia, the whole construct was a "weakly concealed regime of occupation". In the legal fiction of the German government however, it was an autonomous yet integral part of the Reich.

The General Government is a bit different. Here the point was exactly that it represented the Polish territories that were not themselves integrates/annexed into the Reich itself. Hence, its original name "General Government for the occupied Polish territories". The General Government served the only purpose to replace the military administration of the occupied Polish territories that were not illegally annexed with a civilian administration under Hans Frank. According to the 1907 Hague Convention, occupied territory is only territory when actually placed under the authority of a hostile army. E.g. France under German rule was legally occupied as it was ultimately the army that exercised the highest form of control in situ while a lot of the French administration remained intact. Replacing a native administration with a non-native civilian administration as happened in the GG is more akin to an annexation but because the German government wanted to prevent that from happening, they basically invented the General Government. Legally, this hadn't existed before and in the legal fiction of the Reich government the GG was not part of the Reich proper but also not a full state, colony, protectorate or suzeranity; it simply was the General Government. The Reichskommissariate served a similar function as they too went beyond a legal military occupation without becoming a full annexation. They too were purposefully kept vague and slightly undefined in their status resp. the Nazi just made up something which sounded good on paper and suited their needs.

As for the maps: In the end, it depends which view you want to adopt for your maps. In legal history both the Protectorate as well as the GG do not count as part of the Reich but as illegally annexed/occupied territory. In the historic Nazi-German view, the Protectorate was part of Reich territory while the GG wasn't.