I'm trying to get my heli( i bought used last year and just now trying to figure it out) in the air and im having a hard time trying to figure out all the modes and programs so that the radio, esc and gyro will all work together, so I'm trying to tackle it one at a time and the first thing is the ESC and i'm wondering if i have to program it or will it fly on the stock settings?

my setup is

Shogun 400 VI
stock motor
JR 6102
Futaba 401 gyro
Hitec Electron6
CC 25 ESC
hs-55 servos
EF 1600 Mah battery

Not sure about that one but every one I have ever messed with needs to be programmed, at the very least you want to make sure the high and low stick positions are correct or it may spool up as soon as you power it on even with the stick at the bottom, depending on what body parts are in the way this may be a bad thing. Also most ESC's need the throttle channel reversed when using a Futaba radio.

Just follow the directions and you should be ok.