> Hi, how do I download multiple webpages of the same 
> domain, like that each have their own index files
> <http://www.example.com/a/1/>

Set options / Scan rules:
+www.example.com/a/*/

> if i try to download using just <http://www.example.com/> 
> HTTrack only downloads that, not the mulitple sub 
folders, 
> just a load of cluttered files from the main page.

Links must be existing somewhere in the site so that 
httrack can find them.