I had a lot of these same questions!
Ref the charger: the VP4 Dragon is a good charger according to HKJ. His review here:
https://www.candlepowerforums.com/v...3-Test-review-of-Charger-Xtar-VP4-Plus-Dragon. I have the VC4 and like it a lot. Yes, the charger will stop charging the battery when voltage reaches the max of 4.2. The bay indicate light will turn green and display "FULL" on the display at this point. I don't hover over the charger, but check periodically when I'm using it. As soon as I see it's full/green, I take it out. Sometimes that's not until the next AM if I'm charging at night.
My rule of thumb is to use unprotected batteries with lights that provide low voltage protection (i.e. PFlexPro or Oveready).
I insist on using protected (or primary) batteries in lights without low voltage protection (like my Surefire Z2 with Malkoff M61). I don't have a Beagle, but my understanding is that it doesn't provide low voltage protection. So I think you're smart to use the protected cell. There's some good discussion earlier in this thread where @scout24 and @archimedes weigh in on this (starting around post 64).
But my understanding is that relying on either form of battery protection is more of disaster avoidance, and not a good practice. Many of the more experienced flashaholics seem to recommend recharging when no-load voltage drops to like 3.5v. How to avoid reaching this level or know when you have? Here's what I've been able to figure out:
(1) recharge really often just to be safe
(2) pull the cell out of the light and test it on a DMM (not the most convenient)
(3) a lot of experience using and testing the cell which gets you to the point that you just kinda know it's low (not the most precise, and not practical for newbs like us)
(4) realizing when the cell drops out of regulation and output starts to dim (but this will probably be a lower discharge than the 3.5v ideal though, and thus not the best option)
(5) and finally, my preferred - using the voltage check feature provided by some drivers to tell you the voltage without load (again, Oveready and PFlexPro provide this feature - for example, 8 half presses gets you 1 blink for every .12 volts above 3 with Randy's AP driver; similarly, OR has the 111 PIN for batt check) - but unfortunately I don't think this is a feature of the Beagle.
Hopefully you'll get some more detailed comments..