It's not complicated. In most cases you needn't do anything except activate the plugin and set some basic settings as to how big of a lightbox you want and the plugin does the rest. If you are trying to put custom content in a lightbox you might have gotten further by clicking on the little help icons next to each setting. For example
Use Secondary Lightbox: If checked, Lightbox Plus Colorbox will create a secondary lightbox with an additional set of controls. This secondary lightbox can be used to create inline or iFramed content using a class to specify the content. Default: Unchecked
Add Inline Lightboxes: If checked, Lightbox Plus Colorbox will add the selected number of additional lightboxes that you can use to manuall add inline lightboxed content to. Additional controls will be available at the bottom of the Lightbox Plus Colorbox admin page. Default: Unchecked
Once you get that far and tick those off more options are displayed with instructions on how to use them to manually insert content. They are deliberately hidden because for most uses the basic setting which are automatic are sufficient for most people. Additionally there are multiple examples at the Lightbox Plus for WordPress Demos page of how to use secondary and inline lightboxes for custom content.
As for you Mr. Zakharia, I find it quite strange that you have gone, rather obsessively, out of your way to post about how "terrible" the plugin is in so many places including here, Facebook, Google+, probably twitter and who knows where else. If you don't like the plugin, don't use it but otherwise leave off. It's free, as in speech, which does not include support or even that I be clear in how to use the software.
I'm one person working on this, I make virtually no money from it, I get the occasional donation and that's about it. I have other responsibilities which take precedence over development of this plugin and, generally, when time allows, development takes precedence over documentation. If you'd like to write comprehensive documentation for it I would love to have the help.
So rather than complain about how terrible it is, you might ask what you can do to make it better as seem to be rather interested in its functionality.