While I don't know what the "best" way is, I can always give you some advice how I do it when I encounter turbulence in a jet aircraft

Reduce control surface movement and lock the N1. Since the turbulent air will play tricks on your airspeed indicator the most reliable info is the N1 gauge.
Real Boeing's have a pre-set turbulent air N1-setting just for this matter.

Turn on yawdamper if you have one, this system prevents the aircrafts tendency to commit dutch rolls which is more probable to happen in turbulent air.
Some aircrafts (such as the CRJ) has a turbulence switch which dampens the autopilot reaction, other use winglevelers (BAe 146, for example). So what is my point really?
It's simple: don't try any acrobatics  

Whatever 'plane you're flying; when you encounter turbulence your first response - aside from keeping the wings level - is to slow to that 'plane's manoeuvering speed (Va). This speed should be listed in the aircraft's checklist or in the learning center. Too much speed in turbulence can overload a wing and cause it to fail; Va is the speed at which a 'plane can use full control deflection without risking damage. So slow down - it's safer.

One other thing: it's easierst to use the autopilot when flying through chop; it does all the hard work for you.
But you can't get better practice at aircraft handling than by keeping it manual in rough air. Even in FS9 it really helps in developing 'feel'.

cheers!