I'll tell you that on my non-abs bike, if I need to stop quick the rear tire isn't even making contact with the pavement. You may get a little more use out of the rear in an emergency situation with linked ABS but I'm not sure how much since I don't know how the computer deals with percentages and so on. Air in the lines can kill you, don't do it.
As for shifting, you'll figure out what's comfortable and go from there. You just started riding this spring right? So your brain is still trying to process everything as separate actions because it's not muscle memory yet. It's good trying to get into the right habits early but it's also good to know when to just go do something and learn on your own. Like JSchaf said, you want to be at a point where you're not thinking about what your feet are doing, they just do what you need them to and the only way you'll get there is by riding.
On the topic of engine braking vs active braking, I pretty much think of it like this:
If I'm charging corners and late-braking, trying to ride like I'm on a race track, I'll use my front brake to set corner entry speed.
If I feel like I'm coming into a corner a little too hot, I will either use a little bit of front brake before setting my line and dipping into the corner, or I will trail brake rolling into the corner (still need practice on this one).
If I've decided on my pace for the day and want to run at a constant speed/rhythm, I will stick the bike in 2nd/3rd gear (will be different for you) and just let the engine brake for me. Essentially if I don't need to stop suddenly and the deceleration period is fairly loose, I won't ever touch my brakes.