i can't remember exactly, but i did make a customised theme for a phpBB forum a year ago; basically, the design and the actual code is quite well separated, making it "not too hard" or "easy" to modify (the design).
Unless someone tells you exactly what you have to do, either here, or in the phpbb.com community, my advice would be to open a few files which names make sense, and see what is done inside.
Hmm, i'm sure you'll find infos about that on the phpbb.com forums
Custom themes are extremely easy, they use PHPBB's template syntax (which is basic html with variable parsing and basic loops). They're located in the /styles/ or /themes/ folder if I remember correctly.
The files, are .tpl, and can be opened with notepad or any html editors such as dreamweaver. Each file represents each part of the forum, ie overall_header.tpl this is your header... index_body.tpl this is the main index page with all the different sections of the forums are displayed.
Basically its easier to mod an existing template then it is to create one from scratch, as all the files names are set, along with the image file names, just make you new images and replace the old ones.
make your header, with or without the links, if you use photoshop, make sure u use slices, this would break up the design, when done, save to web, and when you selecting where to put it, you will noticed options below, images only ect... make it html and images... this will then give you the html code for the template, paste it into the overall_header.tpl, but only replace it where the html is for the file... normally at the bottom.
There are so many things, to do, just look our the old template is and basically try to make it so with yours.