Store Website Configuration Data?

We have a platform for web applications. The idea is that different clients can have their data hosted and displayed on their own site which sits on top of this platform. Each site has a configuration which determines which panels relevant to the client appear on which pages.

The system was originally designed to keep all the configuration data for each site in a database. When the site is loaded all the configuration data is loaded into a SiteConfiguration object, and the clients panels are generated based on the content of this object. This works, but I find it very difficult to work with to apply change requests or add new sites because there is so much data to sift through and it's difficult maintain a mental model of the site and its configuration.

Recently I've been tasked with developing a subset of some of the sites to be generated as PDF documents for printing. I decided to take a different approach to how I would define the configuration in that instead of storing configuration data in the database, I wrote XML files to contain the data. I find it much easier to work with because instead of reading meaningless rows of data which are related to other meaningless rows of data, I have meaningful documents with semantic, readable information with the relationships defined by visually understandable element nesting.

So now with these 2 approaches to storing site configuration data, I'd like to get the opinions of people more experienced in dealing with this issue on dealing with these two approaches. What is the best way of storing site configuration data? Is there a better way than the two ways I outlined here?

note: StackOverflow is telling me the question appears to be subjective and is likely to be closed. I'm not trying to be subjective. I'd like to know how best to approach this issue next time and if people with industry experience on this could provide some input.