The problem seems to be creating a *new* site. It sounds like your "new"
site has somehow got integrated with the existing one.
If you're working on several web sites in frontpage, you should be storing
them in a file/folder structure such as:
c:\my documents\my webs\site1
c:\my documents\my webs\site2
c:\my documents\my webs\site3
If you view "my webs" in Windows Explorer, you will see the folder icon with
a blue globe - which indicates it is a "Frontpage Web". The "parent"
folder should be "mywebs" (or whatever you store them in) and the "child"
folders are "site1", "site2", "site3" etc. It sounds like you have
inadvertently done something like this
c:\my documents\my webs\site1\site2, so that "site2" is inside site1 rather
than separate from it.
Create a new site (or 'web' in versions earlier than FP2003):
File > New > Site and then name & save it.
FP creates the web folder with some of its special meta data folders/files
(i.e. those commencing "vti" etc). The term 'web' or 'site' in this context
is the FrontPage term for the web folder in which each site is kept. You
obviously know how to publish using FrontPage; so you publish the site you
have open at the time. For each web you want to publish you need to open
that web (File > Open > Site/Web), then File >Publish Site/Web. Specify the
URL to publish to (or FTP server if not using the FP extensions to publish
by HTTP)
Enter your log on details for that web server (details provided by your host
for that particular domain), transfer the file(s).
If the above doesn't assist you, could you provide details of 'how' you're
publishing and what steps you're taking that's leading to the problem you're
having, we can probably work towards a solution.