You'll want Daum's SVN version of dosbox, not the latest stable version.
You need to have an MSDOS boot floppy disk image available, that's the boot622.ima file.
You also need to convert your windows 98SE iso file into a hard drive image, and IIRC WinImage is the easiest way to do this.
The commands at the end of dosbox.conf will need to be commented out in order for you to perform the above steps.
According to the setup at the end of dosbox.conf, a:\ is your MSDOS boot disk, C:\ is your windows98SE install, and D:\ is your windows98SE install drive.
- get your images (create hard drives with the imgmake command in dosbox)
- boot622.ima is an MS DOS boot disk floppy disk image
- drive_c.img is an empty hard drive. Don't make it bigger than 32gb or you can't format as FAT32.
- win98se_installer is a hard drive.
- Once it's created, open it in WinImage and copy the contents of your Win98SE install cd to it.
- edit dosbox config to boot (alternatively, you can just enter the commands manually, but it's annoying)
- Fix paths and uncomment the mount lines in dosbox.conf
- add
boot -l a
- start dosbox
- in dos, switch to d:\ and run win98\setup.exe
- when setup is complete, switch
boot -l a
toboot -l c
in dosbox.conf, and remove references to win98se_installer.img, you don't need it anymore.