Dynamic rmarkdown files are great for one page apps. However, if you have multiple pages/tabs you may prefer to use Shiny with navbarPage. This is a proof of concept that you can render rmarkdown files using Knitr within a shiny app without having to break up the file into parts. It works by using Shiny's renderUI functionality and evaluating the rmarkdown file in the shinyServer environment.
See discussion on Shiny's GitHub page for background: rstudio/shiny#859
I use this approach in a Shiny app that generates interactive quizzes: https://github.com/vnijs/quizr. More generally, it can be used to create multi-page websites that contain text and interactive elements using Shiny and Knitr.
If you prefer shinydashboard there is a minimal working example in the dashboard branch of this github repository by Brandon Bertelsen