Well, first off, I'm not sure why you'd want to put the debug monitor back in when you have a USB-BDM module. Why run ANY monitor unless you're going to set the thing up for use without the Multilink BDM module?
I'm not familiar with the board you're using, but what I'd recomend you do is start by writing simple routines, like set a bit high that you can see happening on your board with an LED or meter. Then set it low. They try to read switches. Then try to send a serial byte. Simple stuff that you can move off to your own little 'library' of routines as you get more and more familiar with the setup you're using. Single stepping with CW is fantastic for learning the 12 and how it works.
Once you know how to control the part, then figure out what you want to do with it, and how you're going to lay out your code to fit.
If you really insist on putting the monitor back it, then do so, but is it really going to be there in your final product?