RT has many ways to customize behaviour and appearence to create custom workflow you need.
RT has many things you control from SiteConfig.
Yes, that's correct, Rights is the powerful tool to control workflow.
You can start your way from Templates and move to Scrips.
Scrips is the next thing you should know about, may be at first you will use them for notifications only, but later you will want more.
Many popular customizations are available as Extensions.
Callbacks are hooks in the web GUI that allow you to hang your own routines to modify how functions are performed and/or display additional information in the GUI. Read CustomizingWithCallbacks.
Overlays are files in which you can replace a function with your own variant or wrap it with custom code. Read CustomizingWithOverlays.
Using the 'local' directory
Under the RT installation tree, there is a directory called 'local'. You can place files under this directory to override most files in the RT installation without touching the original. Read CustomizingWithLocalDir.
Plain old patch files are still a valid way to customize open source applications, which may have its own advantages in some circumstances. Read CustomizingWithPatches.