I can see your confusion bro, it took me all day to get this working on my phone. I'm new too, and the guys that have been around for a while may assume that a certain step or button push is idiot proof but well you know...
so.
Forget about the clockwork app, you dont need it wont touch it for this.
Download everything the thread 2nd init clockwork mod says so that in your external sd card you should have:
lte2recovery.bak and
2nd_init_mod_test.zip
You will also need a file manager installed "rom toolbox" has one, or "es file manager" etc
You should go ahead and download ScriptManager, Plus "AdforScriptManager" that may not be its exact title, but you need SM plus a little addon for it that you should see a prompt for the first time you start it up.
browse to your sd card from your phone (not your computer) and install then open the apk. It will give you a little proggie with 2 options -- Init Recovery and Reboot. Hit Init recovery and you should get a success notice, then hit the reboot button. You will be rebooted into recovery mode. Now you can follow the rest of the steps in the instructions to copy over the zip file, and make the script shortcut on your homescreen. Where the directions say "add sm widget" what it means is long press the homescreen, go to add widget, then scroll to "ad sm" (or similar) when you click it the only option will be reboot_recovery_sh, hit that to make the shortcut. That shortcut is what you will run when a roms instructions tell you to use clockwork recovery, you can even rename it that to remind yourself not to try to use the actual ClockworkMod app, cuz it will brick or factory reset your phone.