Sorry for taking so long to respond, as I’ve said in some other posts, I’ve been sick.
To address your question, it doesn’t really matter how you upload the images, that’s up to you, they just need to be added to a post/page as described in the readme, i.e. [code:2gmqoxr3]<a href="http://localhost/wordpress/wp-content/uploads/2011/01/joe04.jpg" rel="lightbox"><img src="http://localhost/wordpress/wp-content/uploads/2011/01/joe04-150×150.jpg"></a>[/code:2gmqoxr3]
Alternatively, you can turn on autoload, in which case you don’t need to add the rel="lightbox" portion.
I don’t entirely understand what you’re asking regarding an uploaded gallery in WP, if you mean the Add an Image Gallery tab, yes. If you mean something else, you’ll have to elaborate.