Some sites have a common starting page and then they have a
separate site for each section/topic.

Example: 
The main site could be-
<http://www.mainsite.com>

And the other sites could be-
<http://topic1.mainsite.com>
<http://topic2.mainsite.com>
.....
<http://topicn.mainsite.com>

The main page has URLs which take the reader to the other
sites. The actual data comes from these "subsidiary" sites.

How do I set HTTrack?  I tried the following options; and
both didn't work properly:

1. Set the main site as URL, and then set all other sites as
+ ve filters, so that these URLs are captured, also. Problem
here is that other hops in subsidiary sites would be ignored.

2. Enter all URLS in the "URL" box. No filters required. The
problem is that the downloaded pages are not linked as
original or they are even missing (possibly the site expects
a CGI query from the parent site?)

how can I deal with this problem?