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I'm sorry I don't understand. Are you doing the remastering in gentoo?
Also, are you trying to make it so that when it boots up it goes to a terminal and then if you want, you can do startx fluxbox?
I did mine so that it automatically boots up into fluxbox, I think you might have to check the fluxbox documentation on its website.
Here :
There are two generally different ways to start X11 (and thus Fluxbox). The traditional way is using the command startx. The other way is using a graphical login manager (also called "display manager"). The most common display manager is xdm which is part of the XFree86 distribution. The display manager provided by Gnome is called gdm, the one from KDE is kdm.
If X11 is started the former way (via startx), the file that is important is called .xinitrc and resides in your home directory. In the case of starting via a display manager, the file is .xsession which resides at the same location.
The next step is to find the executable for Fluxbox. For most people, this is /usr/local/bin/fluxbox. Now you need to edit (or create) the file I just mentioned. Just put the following line at the bottom of the file:
exec /usr/local/bin/fluxbox
Change the /usr/local/bin/fluxbox to where ever your Fluxbox executable is, the above is the default location when compiling from source. Once that is done, save it and close whatever editor you used to edit it. Now you need to run the following command if you use startx:
$ chmod 700 .xinitrc
In the case of .xsession that is not needed. In both cases, you should create the directory in which Fluxbox stores its configuration:
$ mkdir .fluxbox
If you don't create it, when you exit Fluxbox and restart, you will lose all your settings (the directory is not auto-created unfortunately).
However please note that in the knoppix debian cd, fluxbox is located in /usr/bin/fluxbox if I remember correctly.
Why are you using xnest, is it so that you can have terminals and flux on different sessions? Or is that just for remastering and testing in gentoo?
I'm fairly new to linux so I haven't try xnest yet.
If you want to access terminals can't you just use them in flux w/ virtual terms (aterm looks pretty nice with transparency turned on) 
As I have never used xnest before and I have no idea what your environment of remastering is like, and I don't have much experience at this, I'm sorry
But I'll post the packages to add and remove later on, and if you need anything else that I can help, post in here.
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