There is most definitely a solution to all your questions. Unfortunately I'm not on my linux machine right now so I can't give you my configurations but I can give you some sort of idea. First off you are going to want to check out this link:
Fluxbox Apps File Info
The basic jist of it is the following. Create the following in your apps file
Code:
[group]
[app] (eterm1)
[Layer] {4}
[end]
where:
* 2 - AboveDock
* 4 - Dock
* 6 - Top
* 8 - Normal
* 10 - Bottom
* 12 - Desktop
Now the short cut that launches Eterm should be like this
Code:
Eterm --name eterm1
That will make it launch on the layer that you want. For the ones that you want on a different layer just name them differently and create another group in your apps file. As far as making it not appear on the task bar add this as an option
Code:
[Hidden|IconHidden|FocusHidden] {yes|no}
where:
# [IconHidden] {yes|no}: Hides the app from the icon bar
# [FocusHidden] {yes|no}: Hides the app from the window cycling list used Next/PrevWindow key bindings.
# [Hidden] {yes|no}: is both [IconHidden] plus [FocusHidden]
Now this is all just a summary of the link above, but you should be well on your way. Good luck