This is not a book recommendation, but a recommendation based on the big picture you seem to be asking about and can be taken as complementary advice.

If you are writing a large web application in Perl, I would presume that the application will be developed by a team.

Whether or not it will be developed by a team, but particularly if it will be developed by a team, you don't want your application to be simply a collection of CGI scripts. You'll want to explore putting it in an application server framework, which will

• Save you time and money by allowing your developers to create the application in a framework that saves them from having to worry about such things as how to access the database, how to preserve user state and session information across page views, etc.
• Save you time and money by providing a templating system that will allow your graphic designers to do graphic design that can be easily incorporated into the application by your developers and existing pages to be modified by those without development experience.
• Improve performance and scalability by making proper use of mod_perl in a secure and reliable framework that supports multiple application servers.

I would suggest

• Looking into CPAN modules that accomplish this task (take a look at Template, which I've had great success with, and Apache::Template) and the links mentioned in a previous reply,
• Looking into a commercial package such as Velocigen, and/or
• Finding a consultant who has experience with writing large applications in Perl to get you off on the right foot. I've worked with one consultant, Moon Lee, who has developed a lightweight but extremely scalable application server which has reliably served out gajillions of web pages using both MySQL and Oracle as backends for load balanced server farms, and who I can personally vouch for.

By the nature of your question, I would guess that you are starting from the perspective of someone who has not built large-scale web applications or doesn't have anyone on staff who has. So, based on my experience, I would highly recommend the second and/or third suggestions above. Spending some money up front on a knowledgable and experienced resource will save you loads of time, money, and heartache over the life of your project.

Hope this helps!