Are you hosting your website on a ‘traditional’ hosting plan i.e is it on a linux server, and what is your website address going to be e.g https://www.mywebsite.com and what was your old website address?
If you are hosting your site as suggested above then If it were me I would have a good clear out before uploading a new sparkle website to it.
But be careful what you delete!
in the public_html folder there will be a cgi-bin, whatever you do DO NOT DELETE THIS - sorry about the caps but it is a warning 
Any other files and folders such as index.html and subfolders from the previous iWeb can safely be deleted.
I have never used iWeb so I don’t know how it hosts the files etc. Maybe someone else can also suggest some help in this regard.
Best
Scott