LenAlign can be used with a zoom lens, but because many cameras have only 1 AF Adjust setting per lens, there is an issue if the long and short end of the zoom lens does not perform identically in terms of AF.
The latest Canon cameras (1Dx, 5D MkIII, 7D MkII, 5Ds/R and later) and all Olympus cameras with AF Adjustment functionality have a separate setting for the telephoto end of the zoom and the wide angle end of the zoom. Check Cameras with AF Adjustment for details.
Cameras with 2 settings for a zoom lens.
Test and set the appropriate AFA setting separately for each end of the zoom lens at the appropriate distance for each end. For example a 100-400 zoom would be tested at 8 feet (100mm) and 32 feet(400mm). The order that you test does not matter. Be sure to have the zoom fully set to each extreme end of the lens. if you only test 1 end of the zoom lens, be sure to enter the same AFA setting into the other non-tested end of the zoom, until you are able to test and adjust it.
Cameras with 1 setting for a zoom lens.
Using a 70-200 zoom lens as an example:
The best way to approach the issue of a zoom lens with a camera that only stores 1 AD Adjust setting, is to test and adjust (if necessary) at the 200mm setting. Then test at 70mm and see how the AF is performing. Since there is more DOF at the 70mm setting (unless you are very close) usually there is enough margin for error that any difference in how the AF performs at the near and far range of the zoom. To summarize, generally test and set at 200mm, and then do a quick check at 70 mm at the appropriate shooting distance.
If the AF Adjustment at the extremes of the lens are very different, then you will have to make a decision either to go with one or the other (depending on your shooting needs), or use them both at different times, when using the lens for different purposes. If both ends must be right, then the lens will have to be serviced by the manufacturer to bring the short and long end of the zoom into proper calibration. (Check with the service center to see if this is possible for your specific lens).