If the new D30 will be your front axle, the brake calipers should, directionally, be on the rear of the rotors (on the side closest to the firewall). For rear disc brakes the caliper should, directionally, be on the front of the rotor (on the side closest to the seats). You may have to move some hard brake lines around a little bit, but that should be a minor inconvenience (just don't break/pinch/collapse them). You might also need a coupler nut of sorts to connect the threads, that will depend on the current setup and the D30 setup. Be sure to bleed the brake lines well, and you should be good to go. Oh, remember to connect the axle to your suspension
While you're updating your axles and braking system, you might want to consider upgrading to a YJ brake master cylinder / brake booster setup. Do a Google search for "CJ brake upgrade", you'll find what you need as well as how-to guides.