Appropriate directory for themes, logs and config files

Hello, I would like to know what would be the appropriate directory to place a application's config directory that contains themes, logs and config files for that application.
I want that directory to be accessible but since ~/Library is now invisible on Lion, that kinda rules it out for accessibility. The only place left now would be ~/Applications, but I don't think it was intended for that.
There is also an invisible config file that contains the path to the config directory and that's what the app uses to know where the config directory is located. The current emplacement of that config file is in the home directory, which I think is not in accordance to Apple's guidelines. So where should I place that file?
What should I do?
Thanks

Whee wrote:
I wish I could choose both of your answers as being the good one.
Thanks for the additional info about the Home and Documents directory, that clears a lot of things up. I needed to know that too. Do you know where that documents is located now? http://developer.apple.com/library/mac/#documentation/MacOSX/Conceptual/BPFileSy stem/Articles/WhereToPutFiles.html
Apple prefers you use the system API for these things. Here is one document that explains it.
So even though I won't use NSDefaults because what I am working on is a cross Platform app that is in C, I will put the config file in ~/Library/Preferences and the config folder in ~/Library/Application Support.
Almost everything has a C equivalent. You can use CFPreferences instead. I strongly urge you to use one of the system APIs instead of trying to write your own files. For one thing, the user can put their home directory virtually anywhere they want. For another, Lion is rewriting the underlying architecture with the new screen sharing and iCloud. If you use the system APIs, your program will work properly with any new technologies or custom network settings.

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