Have you found the programer manual yet?http://www2.tek.com/cmswpt/madetails.lotr?ct=MA&cs=mpm&ci=13072&lc=EN
Under the measurement group, you will see there are two types. Immediate and Measurement. The MEASU:MEAS commands are used to set up the scopes display to show the measurement, the Immediate command is used to tell the scope to calculate something, then spit the value back. Typically I recommend using the MEASU:IMM commands for automation, though you can use the others if you want a screen capture showing the results.
In either case, you will need to set the SOURCE1 and SOURCE2 for your channels. The TYPE will be phase. You can then query the value. (examples if the syntax for each of these commands is in the programmer manual). Don't forget however, if your using the MEASU:MESS commands to turn the measurement STATE on as well, or else it will not display on the screen.