For the front, use spacers under the front suspension. CRC has a kit with 3 different size shims.

For the Rear, I use IRS ride height adjusters.
http://www2.towerhobbies.com/cgi-bin...SM&C=CMZ&V=IRR

As far a measuring, I do the front at the very front of the chassis, the rear I do at the lower pod plate between the sidepods. You also want to check the ride height at the rear of the main chassis plate, this height you adjust with the center spring.