I've been doing some research on this, the Walter HWK 109-500 rockets weighed 125kg produced 500kg of thrust each, for a total of 1,000kg of thrust. They burned for 30 seconds and were then dropped via static line parachute. The Jumo 004s produced 903kg of thrust each for a total of 1,806kg of thrust. So to make this work, the aircraft will be set up with four engines - 1 and 2 are the main jets, and located accordingly; 3 and 4 will be stand-ins for the the two rocket motors and located accordingly. Since you only get one set of engine parameters, these will be set up for the Jumos. The thrust of the rockets will be adjusted another way. The visuals will be the two rocket pods, set up as drop tanks. They will weigh a total of 125kg each, and this will be divided between the weight of the drop tank and the fuel that engine 3 burns in 30 seconds. Thus the fuel load for the aircraft itself will remain correct for the rest of the time the aircraft is flying. The rocket pods will have some drag as well. The visual effects will be tied to the engine 3 and 4 effects and located at emitters placed where the nozzle of each pod is located, even though the pod itself isn't part of the aircraft model. The effect will be triggered when engines 3 and 4 start and will last 30 seconds. Sound effects for the rocket motors will be part of the aircraft's sound package, with engines 3 and 4 calling for the appropriate rocket sound files, while engines 1 and 2 call for jet sound files. If you want to add cockpit controls, I understand it was a simple on/off switch to control the rockets, though I don't have a picture of one. It could be tied to engine 3 or 4 throttle position, animated so that with a throttle setting above 0% the switch is in the ON position.
The operation will require a script to be run prior to flight. The player will manually start engines 1 and 2, using autostart will mess up the sequence, so the script will disable that feature. Once the jet engines are running, the player will press a button that the script will use to initiate the rocket sequence automatically, it will also take over control of all engines from the player for short periods of time during the sequence. First, engines 3 and 4 will be started simultaneously, triggering the visual effects, this will also initiate a countdown timer that will shut engines 3 and 4 off after 30 seconds have passed. Once engines 3 and 4 are started, the script will set their throttles to 50% (thus giving them the correct amount of thrust) and then restore control of engines 1 and 2 to the player. The player can then throttle up the jets and start the takeoff. As on the original, the player will be able to shut down the rockets at any point, but has no other control over them. After 30 seconds, the script will shut down engines 3 and 4, the effects will stop and so will the engine sounds for the rockets. The script will also disable all control of engines 3 and 4 for the rest of the flight. The player can then jettison the rocket pods like a drop tank. A parachute effect will trigger on release, though it won't actually slow the drop of the pods.