Brake on/off will control what the propeller does when you pull the throttle to "off". With the brake on, the prop will stop almost instantly and remain in one place until you throttle up again. If you have a folding propeller, this is the setting to use. Brake off will allow the propeller to pinwheel in the wind. That causes more drag on the airplane, but some people prefer theirs set that way, so they can use the free-wheeling prop like a sort of air-brake as they land. Neither setting will affect how the ESC treats your LiPo.
Regarding the programming card, I've given up trying to program any ESC in any other way. Every manufacturer has a different set of beep codes and a different sequence of "up-throttle / mid-throttle /off-throttle for .0002 / 1 / 2 / 5 seconds until you do or don't hear one / two / five beeps making an up / down / sideways kinda sound." To me, the small cost of the programmer card is well worth the retention of my patience. ymmv
I was looking thru the online version of the manual for the "JETI Brushless Advance 30-3P" at
http://www.jetimodel.cz/eng/navody_en/3p_old_eng.pdf (and if that is the exact model you have), it does NOT have LiPo recognition. On the second page, paragraph 10 says, "The speed controller will turn off the motor then the accu voltage falls under 5,3 V or reach 0,7 V/cell. It depends on what happens as the first." (sic) That is TOO LOW for a Lipo, and will cause damage.
Either add a Li-Saver or replace that ESC with the newer Jeti Advance 30 controller or another LiPo enabled ESC. Sorry.