> Question is: can HTTrack save my offline folder in a 
> separate folder from the hts folder...?
Add the -O option, for example after all URLs,
 -O <path-to-htmldata>,<path-to-cache-and-logs>

Example:

www.foo.com -O "D:\My Web Sites\Foo\","D:\My Web 
Sites\Caches\Foo\"

Note: you can also do the mirror on a PC, and opnly 
copy "interesting" folders (www.foo.com)