1. You cannot unghost a site, you can only unghost a page. By default,
all pages in a site will be ghosted (uncustomized). You can, by simply
clicking save in FrontPage 2003 or by altering the properties associated
with an ASPX page in a document library in the browser, unghost
(customize) an instance page. Admin pages in _layouts cannot be
unghosted. This unghosted snapshot will always be different than the
direct-mode page template (found in the site definition) upon which it
was based. Any changes to the direct-mode page template will not be
reflected in the customized instance page.
In WSS v2, there is no OOB way to tell that a page has been customized
(unghosted). However, Maurice Prather wrote the Web Part Toolkit which
contains the Ghost Hunter Web Part. You can download this Toolkit from
http://BlueDogLimited.com and install the Ghost Hunter Web Part from
your SharePoint Web Server. When you put the Ghost Hunter Web Part on a
page, you will see all the pages in the entire site collection that have
been unghosted. The Web Part also lets you reghost pages (abandon any
changes made to the page outside of a container like a WebPartZone or
LinkBar).
2. Customized (unghosted) pages that are included in a custom site
template (STP) will result in unghosted pages in any site created from
that template. Worse, any page that has been reghosted and subsequently
included in a site STP will bleed thru as unghosted in any site created
from that template.
<soapbox>
G-g-g-ghosted is g-g-g-good. Unghosted (in WSS v2) is bad.
mindsharpblogs.com/.../626.aspx
WSS v3 has fixed these problems for instance pages. So, customizing them
with SharePoint Designer (SPD) is fine in WSS v3. However, IMHO,
unghosting master pages in WSS v3 is still not a good idea.
</soapbox>