Braking w/ the clutch in is about the same as braking in the 5AT, so yeah that's perfectly ok.

I'm not sure I understand your second question. You are pressing the clutch and braking at the same time with the stick in neutral? Only feedback I have here is:

1. Once in neutral, you don't need to press the clutch anymore, so don't.
2. Unless you are coming to a complete stop, you will need to use the accelerator to rev up the engine before putting moving from neutral to whichever gear you want to select. You need to rev to whatever RPMs the engine would be in that gear. This isn't that hard, just put the clutch in, rev it up, put the gear in and get off the clutch.
3. I would leave the car in gear while braking unless you are going to go so slow that you are bogging the engine. For example, if you are in 4th gear at 60mph and you brake to 40mph, there's no reason to get out of 4th and into Neutral. Just stay in 4th. If you need to accelerate quickly once at 40mph and 4th is too slow, put the clutch in, rev the engine, and select the lower gear.

I don't know if that's helpful or what you were asking but I took a stab at it based on my understanding... hopefully I wasn't way off

 

So the 5AT and 6MT are nearly the same ratios but adding a sixth gear? Is the 6MT at ~3000 at 70mph just like the 5AT in 5th is at 3000@70? I'm thinking the 6MT is better spaced, because the 5AT RPMs drop more per gear, and then 4th-5th they hardly drop at all.

 

No way not at all. 5th in the 5AT is similar to 6th in the 6MT, maybe a hair shorter. The gears in the 6MT are closer together.

4th in the 5AT is exactly 5th in the 6MT, and 5th in the 5AT is .839 whereas 6th in the 6MT is .794