RE: Do the flight characteristics stay the same..
Pete,
I agree with what both Craig and Tom said. Start slowly and add just some armament at a time, and check the CG each time as the armament itself can change the CG. Most manufacturers don't "balance" their armament, so you may have to add weight to it just to get the CG to stay the same with it on. If you can, I prefer to add the weight to the armament itself so that when you get it all figured out, you can change the configuration without having to add/remove weight from the plane to get the CG right - but that's not always easy to do if the armament is already built and finish painted, etc.
How you build up to a full load is probably specific to an aircraft and what you want to fly with in the end. Missiles are usually small players are far as drag and weight go, so they are generally easy - although some guys have said that tip missiles have changed the flight characteristics of their airplanes significantly. Fuel tanks and bombs have more potential to change things - especially if they are on the wings, I would think. Of course it also depends on the aircraft and its characteristics, wing loading, power, etc. Craig's big Mibo A10 could probably carry the kitchen sink and still fly OK, but a 1/8th F-16 may really struggle with a couple of tanks hung under the wing...
Only one way to find out... Just treat each new configuration that you fly as a "test flight" and be conservative until you know how it flys. Seeing what other guys are flying on their specifi models of the kind you have would be good to.
Bob