I’m using jurabib for citation in the humanities. Since LyX jurabib support is incomplete I’ve come up with the following solution to “hack” the preamble and document. Just include it in a LyX template and don’t worry about it no more.
Update: It was pointed out to me on the lyx-users mailing list that there is a better way to do it. Take a look in the LyX wiki for more on that.