I remember looking for this a while back and not finding an answer, then as i was reading through the gentoo docs, I found what I was looking for.
I wanted a borderless transparent aterm to lay on the desk top layer only and never come to the top on click.
Using Fluxbox 9.14 and aterm 0.4.2 I have foun my answer!
this is what i added to my .xinitrc file to have it load . . .
Code:
aterm -tr -fg green +sb &
Then a placed the aterm window where i wanted, set the size and had Flux save the dimmensions, layer (desktop), position and save on close.
then I closed it and re-edited the .xinitrc to . . .
Code:
aterm -tr -fg green -bl +sb &
restarted X and BAMB!
A borderless transparent aterm where i want it on the desktop.
