Beyond administrative settings and updating or creating content using various modules, most of your visual modifications would be done to by either changing to a stock or custom skin/container set or modifying your existing skin/containers (either ascx or html files) and their associated css style sheets. Although I do not recommend modifications to either administrative or specific module ascx user controls and their code-behind files due to making future framework or module upgrades more difficult, this is certainly possible. Changes done to the code-behind files of the website itself  (including those in the App_Code folder) will be dynamically compiled as the site is loaded.

The implementation of custom features and capabilities not included in the core framework or available in third-party extensions (such as available in the DNN Forge or on the Snowcovered.com application marketplace) are best done by creating module packages and other extensions such as skin objects. Please check out some of the extension development resources in the Wiki, the various blog posts, and the video tutorials of this site.

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Bill, WESNet Designs
Team Lead - DotNetNuke Gallery Module Project (Not Actively Being Developed)
Extensions Forge Projects . . .
Current: UserExport, ContentDeJour, ePrayer, DNN NewsTicker, By Invitation
Coming Soon: FRBO-For Rent By Owner