The statistics for main domain will be included all subdomains and subfolders or they are separated?

they will be in same file with different alias. that mean if the subdomain having the same domain under the same alias then they will be placed on one file. But if they are different, like having different public_html then they will be automatically placed in different file as they will be regarded as differetn alias on the same server.
It actually use the same rules which are used on apache.

Regards

Actually that depends on the Apache.

If Apache have seperate log files for each sub domain, then you can have seperate awstats statistics.