I assume what your trying to do is using eZ Publish classes (the word API is a bit misleading here as we don't have a public api yet in a SDK sense, so API in this context refers to general classes in eZ Publish) outside of the eZ Publish context.
In this context there are two issues:
The autoloader in eZ Publish assumes it is at the root.
Not all classes are autoloaded yet, at least datatypes are left and might be other places as well. This is a long term process getting rid of all artifacts from the php4 era.
Both can maybe be worked around by changing current working directory* before you include autloader and start using classes, but there are no guarantees of it though. * Just adding include path would be enough for class loading, but to make sure misc cache and filesystem code don't break changing cwd is probably better.
