Where do I put new Terminal commands?

Could you be a little more specific please?

What command did you download, and in which form did you download it - as disk image or as .pkg file?

 

use terminal to navigate (cd) to the folder containing the app. Then type the app name and any other switches you need to use. Should work fine.

 

Depending on the setup, you may have to prefix the command with its path to make the terminal look in the right place.

Code:

cd /path/to/application
./command [parameters]

or

Code:

/path/to/application/command [parameters]

Edit: Regarding the OP's question, the command can be put anywhere. It will still be accessible if the place you put it in has been added to the PATH which tells the Terminal where to look for commands. OS X: Change your PATH environment variable

 

If you will use the command a lot, you can copy it to you /usr/bin/ or /usr/sbin/ folder. Then you can run it just by typing in 'ipodpatcher' regardless of what directory you are in. You can copy it like this:

Code:

cp /path/to/ipodpatcher /usr/bin/ipodpatcher
chmod 4755 /usr/bin/ipodpatcher

The first line copies your binary to the /usr/bin/ folder and the second one changes the permissions of the file you just copied so it can be executed. I can't remember if either of those commands requires root permissions, but if you get an error about permission being denied, just prefix each of those lines above with 'sudo' and type in an administrator password when prompted.