Love my Atahualpa theme [just wish I knew what Atahualpa meant.

]. Since 1/11 I've developed a site I'm quite comfortable with. However, I realized it now covers 3 main topics, and wish to segregate them it into three sibling sites. There will be cross-over pages/wigets/categories/tags & posts the three still need to share. Therefore, I thought the best way to handle this would be to convert my site to a multisite network with unique sites n unique urls. That way I could share data and still give the user a unique experience for his/her targeted area.
However, I don't want to use this approach if I will lose any ATO functionality in the process. So, if I convert my site to a network of 3 sites, still using ATO - just with different header images and slight color changes, will each still work as they do now? Anything I need to keep in mind about using ATO before I make this change?
Thanks.