you should try to make sure the cables are properly seated all the way in the original harddrive, then if it still gives you that error, then pop in the floppy, and at the command prompt type this: C: /chkdsk
then hit enter, IF your hardrive is being recognized, it will go through a series of checks to make sure the data is not corrupted and boot you to windows.
As far as adding a second harddrive, they normally come preconfigured from the factory as 'Cable Select' on the jumpers, and so all you do is add it to the second ide connector found on the cable that plugs in to your existing harddrive, if you moved the jumpers on the original and DID NOT properly return it to master OR cable select, that may be your problem.