If you feel comfortable with your current WB setup then keep it - I don't want any blame for messing up your system!
The truth is without knowing what you've got installed it's hard to say. The WHDload games could be left on the HD no problem, just be sure to back up the WHDload key file (if you have one) as you'll need to drop it in the c directory once the classic WB is installed.
Truth is I was only pointing out an option and it's really up to you. If you're happy with your WB setup then DON'T change it - after all it's main use is probably launching WHDload games anyway!