I am not sure, this is fvwm2, and I've never needed to set this manually for any app. New windows so far are either placed on some empty part of the screen or under the mouse cursor. And I am happy with this. Now, LyX doesn't do it that way...
Maybe it is really a generic problem I've never encoutered before and the fact that LyX wants more than half of the width of the screen and not much free spaceadds to the problem.
I tend to use a narrow lyx window, with xdvi on the rest of the screen. Lyx popups is something I pile on top of the xdvi window. I use mouse focus and no autoraise. The latter is just a disaster with lots of semi-overlapping windows. (I have lots of other windows too.)
Quick check: Both Mozilla and Netscape keep the 'Find' dialog always on top.
Which is a nuicance, having to cancel the thing instead of jsut clicking on whatever I want on top.
Helge Hafting