You can create a subdirectory "www" under your application directory, and place a .css file there. Then reference it from your ui.R. For example,
~/myapp/ui.R
~/myapp/server.R
~/myapp/www/styles.css
In your ui.R you can put a tags$link anywhere, for example in mainPanel:
mainPanel(
tags$link(rel="stylesheet", type="text/css", href="styles.css"),
# more controls go here...
)
That tags$link will become:
<link rel="stylesheet" type="text/css" href="styles.css"/>
Notice that while your styles.css is stored in a www directory, you do not reference "www" in your link tag.