After testing a number, actually most of Honda's hybrid models except the MMC Insight and the Jazz (Fit) Hybrid (I will get my chance in August), my opinion is that 'brake charging' is best accomplished by getting into closed throttle without braking or with as little braking as possible.
I notice that when you properly engage the brakes, the charging is reduced. But at closed throttle cruising, or coasting down, the ECU uses the charging to create the 'engine braking' effect.
In models like the CR-Z, actually all IMA models by now, when the throttle is closed, the engine 'shuts off', the valves are deactivated and there is no fuel flow. This saves fuel and improves fuel consumption.
Then to create the normal engine braking effect, they start charging the IMA battery. The retardation from the IMA motor now running in reverse mode as a generator creates that effect. But it is limited as it is only a charger and not a true retarder, i.e. whatever resistance is there due to the charging process only.
So once we need more braking power, we need to properly press the brakes, which now comes into play. For some reason, the charging now almost shut off by the ECU.
In my test of the CR-Z, I ran down the battery charge from variously, 6, 7, even 8 full bars with a only a few runs for 0-60mph tests. After that, I just took a drive on the roads around the test area (it was an isolated road located off an equally lightly traffic'ed area on weekends). What I do is I accelerate quickly up to some speed and then simply coast around, letting the charge meter go to maximum as much as possible. It was possible to go from 2 or even 1 bar back up to 6 bars with only a couple of minutes of coasting like this.
Of course, all these are from just review driving experience, over an extended weekend (Fri to Mon), not real owner experience so YMMV.