First make sure that your minecraft is closed during the process.
Then you unzip the texturepack into a new folder so you are able to access the textures and make changes.
Now you go into the alternative textures folder which is at the pack at: assets\minecraft\alternative textures.
There you can take a look at all possible (provided by us) alternative textures. 
As soon as you selected some textures you want to apply to the active pack you have to replace the currently active texture 
with the alternative texture you want it to repace with. 
Also you have to make sure you use the original texture name! Otherwise it WONT work. 
As soon as you are finished changing textures you have to zip the changed assets folder (which includes all you changes then), 
and put the now zipped pack into your minecraft resourcepack location.