What version of Publisher?

Are you familiar in using a ftp?

Not sure I understand what you are asking, but if you want to replace an
existing site with a new site you produced with Publisher then you need to
delete the old HTML files on the web server and upload your new files.
Perhaps these articles will get you heading in the right direction:
"Prepare, publish, and maintain your Publisher Web site":
http://office.microsoft.com/en-us/assistance/HA011053521033.aspx

and articles by David Bartosik on uploading your site:
http://msmvps.com/blogs/dbartosik/archive/category/1921.aspx

If you have included a form on your site, you will want to use HTTP
uploading protocol.

DavidF