Think of /Library as Apple-sanctioned, and /usr/local/* as generally third-party installations performed in the terminal. Your Python install is likely the install that comes with your Mac as bundled by Apple. Therefore, it doesn't really know about libraries that you've installed yourself. You can set sys.path in your python apps to tell them where to load libraries from. You can also use sys.path to see what the default path is:
>>> import sys
>>> print sys.path
Another route you can also take is to use a third-party package management system to install all of your development versions of software to get more fine-grained control of what libraries you want installed. This also allows you to update to newer versions of libraries than what Apple provides. MacPorts and Homebrew are two such package management systems.
So, in your case, you are interested in Tk and Python. You could use MacPorts to install your own version of Python and Tk, and use those versions instead of the out-of-the-box versions. Because these packages are installed by the same package manager, the MacPorts version of Python will be aware of any other python libraries installed by MacPorts.
Using a package manager means that you'll need to do some things such as setting up your $PATH to use the software provided by the package manager, so be sure to read the docs and get a good understanding of what you'd be getting yourself into. :-)