3 simple steps:
Burn each floppy to CD as a bootable image using Nero's bootable CD option
Enable boot from CD on PC
Use each CD just as if it's a floppy (on booting it should ask for the second diskette - just insert the 2nd CD)
The reason I think you need to create 2 CDs is that in making the CD bootable, it creates a special area that emulates another (bootable) device (e.g. a floppy) and the files that you copy elsewhere on to the CD are not visible. So, as far as I can see, there is no point in adding the second floppy as data to the 1st CD as you won't be able to access it. Following on from this, you can't just make CD 1 after the style of a bootable floppy and then CD2 as an ordinary CD - the contents of the second CD need to "appear" as if like a floppy (but on a CD) as well and burning it from Nero as a bootable image (even though the second floppy isn't actually bootable) is the way to do this.
There is a more sophisticated way of getting it all on a single CD - I think this link click here gets into it. But as it says - it's for situations where you want to regularly make bootable CDs.