Open the data-1.1.0.pk3 (but never change that file itself!), find the model you want to replace, create an identical folder structure to where the file is in the data-1.1.0.pk3, put your model in the newly created folder/subfolder and zip that whole thing up, then rename it to .pk3.
For example if you want to replace data-1.1.0.pk3/models/weapons/blaster/blaster.md3, you need to:
create models/weapons/blaster folder & subfolders,
put your own blaster.md3 in there,
compress your models/ folder with the stuff in it to a .zip,
rename to z-myblaster.pk3 or something (the file name has to be alphabetically after data-1.1.0.pk3).