I understand why there is a partition during the dancing of a wedding. But why do I often see separate seating during the ceremony of a wedding? Is there any Jewish source that dictates this custom or is it merely a custom amongst some communities? It just seems odd because those seated during the ceremony are neither dancing nor praying nor are part of the minyan (presumably the minyan is made up of the men under the chuppah).
The reason for the separate seating is in order that the men and women should not mix. If the men and women will be sitting together and intermingling, especially when everyone is dressed in their finest beautiful clothing, and the women are wearing makeup etc. It is going to cause men to gaze at the women, and that they shouldn’t have improper thoughts. True, when everyone is sitting and watching the chuppah it is not as strict as when the women are dancing, because then they are making all sorts of body movements, Nevertheless, for the men and women to sit together will lead to no good things. This is the correct custom according to halacha. The Talmud in Sanhedrin 20a says that even at a funeral, which is a sad time and people are not pulled to frivolous behavior, that the men and women should stay separated. We also find this idea at a lecture, that the two genders should be separated. Therefore whenever there is a gathering of people together, the two genders should stay separated, in order to avoid frivolous behavior between the genders, which can lead to many inappropriate things.
As a side point, the Chofetz Chaim (Ahavas Chesed 3-6 second comment) says that when the chasuna is done in a tznius way, the shechina (divine presence) is there and it blesses the couple, but if there is too much mixing, the shechina leaves and it has a detrimental effect on the couple.
Rambam Hilchos Avel 12-11, Shulchan Aruch Orach Chaim 315-1, Bais Shmuel Even Haezer 65-3, Sridei Aish 2-8, Igros Moshe O:CH 1-39, Es Tzinuim Chochma 2 pg. 522,