It depends a lot on the production company.  I've talked to some actresses about it, and some others.  My understanding from these people is that, with most production companies, when a scene is made, they film it multiple times just like a "normal" movie or tv show and then someone in the editing room puts together all the best shots to make the final product.  What they also do is take the shots that don't show genitals, that aren't used in the x-rated version, and use those shots to make the softcore porn that's sold to the markets that then sell to hotels, and other places that want the softcore version.  

Some of the studios though do it differently:  
Sometimes, they make the softcore version at the same time they make the hardcore version, but it's filmed separately.  That is, they do the scene hardcore, then they do the scene softcore and the cameras do different angles.  And sometimes it's with different girls and they don't actually have sex.

Some production companies specifically make only softcore videos.  I'm not sure about those scenes but it's quite possible that in those films the actual sex is faked.  I mean, why bother having sex and an actress who is making softcore only probably has it written into her contract that she won't do actual sex.

As for whether or not porn counts as actual sex... that's somewhat debatable anyway.  You ought to listen to Evan Stone's take on the whole subject including how softcore porn is made (linked below).