Doug, in short [very short]:
Capture NX's UI and work-flow is an acquired taste. As with other acquired tastes it comes as an epiphany and with great rewards. Unless you need compositing capabilities, which CNX does not have. You can spot-heal but this is very limited [Colorize, if you want to know].
You should read the CNX tutorials available through Nikon's Web site [Support]. You may also be interested in Jason Odell's very good eBook on Capture NX, though that is not available for free.