I am using Sitecore 8.1 with WFFM. Can anyone please explain me how the multi-site information get saved in FormData?.
As per my understanding FormData will get saved with FormID and its Fields in MongoDB collection, how do we know from which multi-site that form is belong to?.
Also is there any relation between any other collections which has the site information along with FormData?
I don't know of an out of the box solution for this. The "site" is not stored with the form data - you only get the form id.
You could create your own reporting. With the formdID, you can get the form item from the Sitecore database. If all your sites have a distinct form root set (more info on this here: https://doc.sitecore.net/web_forms_for_marketers/setting_up_web_forms/installing/multisite_implementation_with_web_forms) you could detect to which site the form belongs (collect all form roots and see which one matches a parent of the form).
Another solution could be to add an extra (hidden) field to all forms where you store the site. This way you could have the information in the forms database - as a field and not a real property though. And if you don't want the form creators having to add this hidden field, you might also be able to hook into the save pipeline and add the information there - although I never tried this myself.
