Popriv,

The easiest way is to use an incidence meter to set stab, wing, and thrust settings. An incidence meter is a good investment having been a great tool for me for years once I realized its true values. You can setup thrust lines using a level and a protractor albeit more difficult. Building them straight from the ground up certainly results in more enjoyable flying.

Your on the right track in getting your airplane setup correctly. Personally I try very hard to get everything setup mechanically correct first before ever going to the computer mixing. Centering the trims via linkage adjustment as much as possible to ensure the greatest mechanical advantage for the servos. Take your time use the trimming information above taking everything one step at a time. Test fly between changes being sure to take notes as to what you have changed and how much so a change can be easily be lessened or reversed. Your end result will be a good flying machine.