My sites are identical - each has it's own checkout; you can't create an order on one site and then check out on another.
So the content is [for me] the same on all sites - for me.
But you can, of course specify which products go on which site, etc.
No matter which of my domains you visit the pages all look the same - I just want as many options as possible to be seen and attract customers.
My main site
http://www.malikstores.co.uk has been going a long time and the others added about three years ago. So the main site gets all the best Google ratings. Though others do sometimes rank quite well.
I guess I think of this as a number of independent sites able to share data if wanted.
Also, each, able to having it's own identity as well and being able to create a different look and feel for each, including for example, each having a different payment provider.
I must say, once you grasp all this it is a truly awesome set up giving the administrator a phenomenal amount of control.
Apart from that there's not much I can say about search engines.
As for the forum, so many of us have used this cart for so long that we do not find the time we should to help others.
Good luck with yours
Chris