You can move your BeOS system to a logical drive within your extended partition.
Using PartitionMagic, fdisk, or other partitioning software, create an empty logical drive within your extended partition. You’ll probably want to allocate space for it at the very end of your hard disk.
Format your new logical drive as a DOS partition and label it with a name of your choice, let’s say „FREE“ for example.
From within BeOS, run the Installer application.
Install a new BeOS system onto your new „FREE“ logical drive. Installer will copy everything from your basic BeOS system to the new drive/partition. At this time you can block your new logical drive any way you want (let’s say 4K) and also rename your partition/logical drive from „FREE“ to „BeOS New“ for example.
You can also choose to boot this new partition by default via the Boot preferences panel by launching it and choosing „BeOS New.“ Voila, BeOS is now within the extended partition!
You can use the DOS/WIN CONFIG.SYS menu options (see example below) to launch the BeOS from AUTOEXEC.BAT. Use the variable %config% within the AUTOEXEC.BAT to branch to the piece of the bat file that runs the BeOS launcher. It will find your logical drive with the „BeOS New“.
The logical drive with BeOS is not visible from your DOS/Windows partition.
Be Happy.
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Here’s my autoexec/config.sys setup, which you can use as a template to configure your own system:

CONFIG.SYS:
------------BEGIN OF CONFIG.SYS-----------------------------------
[MENU]
menuitem=NORMAL, Windows 98
menuitem=BEOS, BeOS Intel Release 3
menuitem=DOS,Win98 with DOS CD drivers
menudefault=NORMAL,30
menucolor=0,3
[COMMON]
DEVICEHIGH=C:WINDOWSCOMMANDANSI.SYS
[DOS]
DEVICEHIGH=C:TOSHIBATAISATAP.SYS /D:OEMCD001 /N:1
[NORMAL]
[BEOS]
------------END OF CONFIG.SYS---------------------------------
AUTOEXEC.BAT
------------BEGIN OF AUTOEXEC.BAT-----------------------------
@ECHO OFF
PROMPT $p$g
@ECHO C:AutoExec.Bat is starting... (WIN98)
SET TEMP=E:TEMP
SET TMP=E:TEMP
SET winbootdir=C:WINDOWS
SET WIN$=C:WINDOWS
SET PATH=C:WINDOWS;C:WINDOWSCOMMAND;C:
SET PATH=%PATH%;D:SOFTWARE;
goto %config%
:BEOS
D:BELAUNCHLOADLIN D:BELAUNCHBEOS
goto END
:DOS
C:WINDOWSCOMMANDMSCDEX.EXE /S /D:OEMCD001 /M:16 /L:Y
goto END
:NORMAL
:END
---------------------END OF AUTOEXEC.BAT---------------------------