If I am reading you correctly, you want to make a VM using a current Win98 hard drive which has all the installed programmes on it?
You would need to make a bootable
ISO of that hard drive
Do you have the original Win98 CD? (This would be my preferred method of doing it - installing afresh from the Win98 CD)
If you do all you have to do is install VirtualBox onto PCLinuxOS, using getvirtualbox from the repos. (or install Virtualbox on whatever system you choose)
Then when VBox is installed, you can create a new VM using your Win98 CD.
When that is all done you will have a "Virtual hard disk" (just one file) which you can then backup(s) so you have a "clean" version of Win98 which can be used
Another method of backing up the the VM is to use Export.
I normally just make backups of the hard drives which allows me to use that drive when needed.
Please be aware that you should check the MS Win98 license to see how many PC's you can use it on