If you decide to overwrite you existing windows you shouldnt use the same username or it will overwrite your files, if you use a different one there will still be a folder in your 'users' folder (in XP not sure about 98) that has your my documents ect in.
Once you have reintalled windows none of your programs will be on the start menu so you need to reinstall them all.
The best way to do it is to overwrite you windows then backup the files you want to keep and then format the harddrive and install windows clean, as this can help avoid problems caused my directly overwriteing windows.
hope you fix it