If I understand your request correctly you want the footnotes always to appear on bottom of the page? This is what usually should happen, if you do not use \raggedbottom or similar (irrc).
Try to use the footmisc package. It is probably in your latex-installation, if not install it from ctan. (http://mirror.ctan.org/macros/latex/contrib/footmisc) Write something like this is Documents->Settings-->LaTeX Preamble \usepackage[bottom]{footmisc} To learn more about the footmisc (it has a lot of options): http://mirror.ctan.org/macros/latex/contrib/footmisc/footmisc.pdf If this don't work we would need a small lyx file demonstrating the problem. And please do not top post. It makes it less likely for some of us older folks to reply ;-). (and it is much easier to follow a thread in mail-archive when inline quoting is used, just try it :)) hth, Ingar Pareliussen