Sure, just close all windows in the 99 program and go to File, Utilities, and Verify your data file first. Them make a couple of good Backups on freshly formatted floppys. Never try to upgrade a corrupted file or convert your file without a couple of backups of the original file. Next, I would recommend installing the new program in it's own separate folder by taking the Custom Install instead of letting it default to the Programs/Intuit/QuickBooks folder. That way you will have both programs on your computer and each one will run on it's own. Once installed, start the new program and open the Sample Company and register the program from the File Menu. Once registered, download the program updates. Then close the Sample company.
Now, go to File, Restore, and restore your company file from one of your Backup disks to the newer version. It will ask you if you want to convert the file. Say Yes. You DO NOT have to create a new file first. Just do the Restore. This way if anything happens, you can still go back to your older version and company file. Later on, you can uninstall them if you need to get the room back on your hard drive.