First of all, as a rule of thumb: Hidden Scorpion = Happy Scorpion. They aren't flashy, attention seeking creatures like dogs or the rather annoying cat trying to sleep on my laptop right now. They hide while you're awake, and come out to play when the lights go out. You have to remember these are nocturnal creatures that also burrow.

Yes, when a female has babies she will be very protective of them until they're no longer riding around with her. The best thing to do, if possible, is to move her into a separate tank if you think she's gravid (she'll look ridiculously fat, with the "grey" skin like bits showing between the top plates- either fat or gravid, it can be hard to know). However, emps have a very long gestation period- 9 to 14 months, I believe (though 10 months is average). However, I know of several people who have been very successful just leaving the mother in with her buddies. I know one of the users here found that the female was cool with other females, but chased the male off.

No, do not take substrate away. Emperor scorpions are burrowing creatures, they because it's what they're told to do for survival, and it's how they live. Would you want to live in a smaller house? Probably not, and neither would your scorpions.

From what I've heard, the easiest method of breeding scorpions is to keep one male in with one or more females. They'll breed, really no need to worry about that. What you'll need to worry about is the babies, they need it to be warmer and more humid than the adults if you want them to thrive. Even then many won't make it, they're very delicate creatures as babies. However, I assume if you do it properly then you should end up with some surviving babies.

Like most pregnant creatures, momma scorp is going to be very munchy, so you'll want to feed her plenty. I've also heard that causing stress when she has her babies will make her more likely to eat them. So try to keep things relaxed when she has them.

Well, that's about all I can tell you, hope it can answer some questions. I'm certain others are much more informed than I, so do search around a bit!