In preparing for the meeting with Eisav Yaakov took three measures. He davened to Hashem, he sent a peace offering to Eisav, and he prepared for war. How did he prepare for war? He divided the group into two so that if one is attacked at least the other one can escape. There are a number of things that are unclear about this. First we see that when they met Eisav they were all together.
Second, it says Vayachatz twice. Once they day before they met and then again the day they met. Third, we see that they all crossed Ma'avar Yabok together on the night following the day that they were divided. The Netziv answers that Yaakov divided up the group because he was expecting Eisav to attack on that very day. When he understood that Eisav wasn'tgoing to attack that day and had his camp rest before the big meeting, Yaakov gathered both groups back together again and crossed the Yabok. After his bruising battle that night with Eisav's Malach where he came out victorious he was no longer scared of Eisav to the degree he was the day before. The next morning before meeting Eisav it says again that he divided the children. The Netziv says this wasn't the division of yesterday.
This was simply a division into groups as a minor precaution. They weren't separated and all groups stayed together. Why? Because although Yaakov knew he was not facing annihilation, he was afraid of the damage that Eisav could cause him, just like the Malach left his mark by damaging Yaakov's Gid HaNasheh.