You can use various COM objects to do an SQL backup or there is the command-line osql utility.
Creating a backup with these methods isn't terribly difficult but restoring can be a little tricky. What I reccomend is to create a batchfile which stops the MSDE engine, makes a file copy of the master and VC databases and then restarts the service.
There are downsides such as VC will not be able to talk to the database for 30-90 seconds. Since an MSDE engine isn't supporting clients or hosting additional databases this seems a fairly reasonable lapse in VC availability. Write the batchfile and schedule it in Task Manager for off-hours. Restoration at this point becomes very simple. Just intsall the MSDE, shutdown the engine, copy the backed up master and VC databases back and restart the engine.
@ECHO OFF
: Create Backup Folder (Just one example)
FOR /F "TOKENS=1* DELIMS= " %%A IN ('DATE/T') DO SET CDATE=%%B
FOR /F "TOKENS=1,2 eol=/ DELIMS=/ " %%A IN ('DATE/T') DO SET mm=%%B
FOR /F "TOKENS=1,2 DELIMS=/ eol=/" %%A IN ('echo %CDATE%') DO SET dd=%%B
FOR /F "TOKENS=2,3 DELIMS=/ " %%A IN ('echo %CDATE%') DO SET yyyy=%%B
SET date=%mm%%dd%%yyyy%
md "c:\backups\%date%"
:Stop MSDE
net stop "SQL Server (OFFICE SERVERS)"
:Copy the Databases
copy "C:\Program Files\Microsoft Office Servers\12.0\Data\MSSQL.1\MSSQL\Data\*.*" "C:\backups\%date%\"
:Start MSDE
net start "SQL Server (OFFICE SERVERS)"
You should test the syntax using your own configuration information and also do a test restoration before using this for anything important as I haven't tested it with newer versions of MSDE.