Hey There.
First of all, congratulations, now get yourself a pair of safety glasses and wear them, all the time. I'm seriously not kidding about this, it is one of the most important things that you could overlook and when you are just starting out with this the chances of an 'incident' are very large, bordering on certainty.
Then, to give you some pointers I need to know a bit more about your machine, what size machine do you have, what is the working volume, stroke, power of the spindle motor and the kind of drive you've got (servos ? steppers ?).
Is it a production machine or a rebuild ?
What kind of materials do you intend to work ?
What kind of workpieces do you intend to make ?
Are you going to program the machine directly or are you going to set up a whole chain ? (cad package, translator, machine controller)
-- do you know cnczone.com ? --
Strike that, missed you mentioning cnczone in your comment.
I think cnczone is by far the better forum for these kinds of questions, the people there have spent collectively multiple 100's of lifetimes programming, building and debugging cnc gear, this is a very interesting field to play around in.
--
In the few leftover hours that I've got I'm converting this rig:
http://pics.ww.com/d/93690-2/dscf1225.jpg
To a modern simultaneous 4 axis controller. It's been lots of fun so far but rather a whole lot more work than anticipated.