There are a few ways to handle mods.
1.) Backup your current packages folder and then move the new textures in.
2.) Rename the textures that are being changed and then move the new textures in.
3.) Make use of the mods folder.
3a. Go to your AssaultCube folder and open assaultcube.bat for editing.
3b. Right before "%1 %2 %3 %4 %5" you want to add "--mod=mods" without the quotations.
3c. Paste the new packages folder into the mods folder.
1.) Backup your current packages folder and then move the new textures in.
2.) Rename the textures that are being changed and then move the new textures in.
3.) Make use of the mods folder.
3a. Go to your AssaultCube folder and open assaultcube.bat for editing.
3b. Right before "%1 %2 %3 %4 %5" you want to add "--mod=mods" without the quotations.
3c. Paste the new packages folder into the mods folder.