You can do a lot by customizing a theme. For instance, I am currently customizing two different themes for galleries on two websites, and in each case, I'm not too far off.
For instance, take a look at http://stjamestheapostle.ca
and http://stjamestheapostle.ca/photos
In a nutshell, the website itself is made with lots of included files. The site-wide menu, the left sidebar and the footer are in three files that are included in all pages, and almost all formatting is done with style sheets.
As for the "photo" section, I worked exclusively with files in the /themes/myTheme folder (where myTheme is a copy of your theme). I have done minimal adaptation to the theme-related stylesheets, mostly to remove stuff that is conflicting. In each of the pages of the theme (album.php, footer.php...), I added links to my own style sheets at the top, and included the common parts of my site such as the site-wide menu and footer to the appropriate pages of the theme.
Because I haven't coded anything in the program itself, I shouldn't have any problems when I upgrade to Zenphoto 1.4.2, or even to 1.5