Win98 1st ed to Win98 2nd ed

I've got 4Gb, 333Mh, Toshiba laptop that has an OEM Windows 98 1st ed
on it. Purchased from an independent computer store.
I also have a legal Windows 98 second ed CD, full ie not an upgrade
version. Because I want a more modern version of Windows 9x, better
support for USB etc but not Windoze ME.
Can I install Windows 98se over Windows 98 1st ed without wiping out
all of my installed programs in Program Files.
As i remember Setup.exe may have certain switches to install Win98 to
my preferences. Probably a dumb question but I've used Win XP almost
exclusively for the last two years, I remember little about the Win 9x
setup.
As I have a CD rom drive that is sometimey ie sometimes it works and
sometimes it don't. I will copy the entire Windows 98se the
C:\Windows\Options\Cab directory and run the installation from there.
Additionally I've got drivers from Toshiba the video card, for sound
and modem.

Aside: The main reason I do not want Window ME is no native DOS
support. If I'm going to run Windows 9x I must have a command prompt.
On a previous installation of ME on another machine. the workaround or
patches I downloaded to get support for DOS did not work.