Make a boot disk (or download one) that has sys.com and xcopy on it as well as the drivers for the CD drive and mscdex.exe to assign the drive letter. Boot to the floppy, use sys.com to make the C drive bootable (which assumes it is formatted and active already of course), then copy all the files to the C drive (aside from the basic DOS files like io.sys since they're copied when you sys the drive).
Before doing that though, edit the config.sys and the autoexec.bat on the floppy (assuming that the disk is already set up so that the drivers load automatically) and make sure they start to point to C: and not A:. And make sure you copy config.sys and autoexec.bat to the C drive as well. Then when you reboot, have the CD drive in, and it'll all load.
Note that a standard Win98 startup disk carries all the drivers you'll need, but I can't recall if it has sys.com on it, and I'm pretty sure it doesn't have xcopy on it. So you can just make a Win98 startup disk and there should be space for those two programs to be added on (don't forget you can delete some of the files the startup disk carries, like the drivespace driver.