It does not matter where you want to integrate plogger gallery into. The thing is that you have to include the gallery.php file on the first line of your page (where you want to integrate plogger gallery into).
Say you put your plogger installation file into /plogger folder and you have your own main.php file to display plogger gallery. The first lines on your main.php file should be: <?php include("gallery.php"); ?> or if you have your main.php file outside the plogger gallery then the first lines on your main.php file should be: <?php include("path/to/gallery.php"); ?>
Change the path/to with your path to your plogger folder.