So you want to make it the hard way, up to you ! You'll have to do manually what is normally done automatically by phpGraphy.
Create a .thumbs/ subdirectory under the directory where you've your original pictures.
Upload thumbnail version of your pictures into the .thumbs/ directory following this naming convention. Add the thumb_ prefix followed by the original filename (eg: for a file named test.jpg, upload a thumbnail named thumb_test.jpg).
Upload low-resolution version of your pictures into the .thumbs/ directory following this naming convention. Add the lr_ prefix followed by the original filename (eg: for a file named test.jpg, upload a thumbnail named lr_test.jpg).