Matthew Paris and an Italian Franciscan named Salimbene di Adam both wrote in their histories that there was a last-minute marriage between Frederick and Bianca when Frederick was on his deathbed. When Manfred was born, however, Bianca was not married to Frederick, and so Manfred is considered an illegitimate, or "natural" son of the emperor.
Frederick certainly considered Manfred his son, with all the privileges a son of the emperor should have. Frederick's will named Manfred as Prince of Taranto, the "heel" of the Italian peninsula (dark green in the illustration) which was part of the area known as the Regno (the island of Sicily and the southern part of the Italian peninsula). Frederick's son Conrad IV by Isabella II of Jerusalem was named king of Germany and Italy and Sicily. Manfred was a vassal of Conrad and would act as regent in Sicily when Conrad was away.
When Frederick died in 1250, Manfred worked to quell any unrest, and tried to repair the relationship with Pope Innocent IV, who had clashed with Frederick over many issues and felt that the Regno was a danger to the Papal States and should revert to papal control. Innocent was not inclined to be nice to that dynasty, however.
Conrad arrived in the Regno in 1252 and quickly asserted his authority, taking fiefs away from Manfred and reminding him that he only had authority in Taranto.
Conrad had a young son born in 1252, also named Conrad but referred to as "Conradin" or "Conrad the Younger" to distinguish him from his father. Conrad the father asked the pope to be Conradion's guardian, along with a German baron, Berthold of Hohenberg.
Conrad died from malaria in 1254 and Manfred declared himself in control of Sicily, clashing with Innocent. Innocent agreed to recognize Conradin as the legitimate heir to Sicily and have Manfred be Conradin's regent, but Innocent was still Conradin's guardian. Once this was settled, Innocent made clear what he thought of Manfred by excommunicating him.
This would not be the only excommunication Manfred would suffer, but he wasn't going to accept his fate with humility. He decided the best course of action was to strike back at the pope. We'll see ho that worked out for him tomorrow.