So this may seem like a dumb questions but can I only use the template.h and template.cpp to make my projects or can I treat it like a normal c++ project with multiple headers and source files?

You can add more, but you will need to edit the Android.mk file and add the .cpp files (but not the .h files) to the sources list. And make sure that the includes path points to the folder containing the .h files.

do my #includes need to have path names? ei #include "jini/text.cpp"?

if your #includes are already in the JNI dir just put in text.cpp