When you homeschool, each child is in a separate class even if you have some time with all the students--after all, you don't separate your family life between boys and girls even though you probably do have certain activities in which boys may gravitate to and others which girls gravitate to. (For example, you need to shop for new clothes: You take the boy one day because he really doesn't want to go but has to in order to make sure the clothing you choose fits; while the girls want to go and try on many different clothes to help you find the outfits that are just right.)
There should be no problem with homeschooling your boy over the next 17 years (remember that it might not officially be "homeschooling" until the age the State commands that he be in school, but he will be learning nevertheless) along with the girls in the household.
The family needs to stay together, pray together, and learn together.