The best solution is to get a Universal Remote Control that can communicate and operate both your old and new components, and can be updated as new components are added. One example is the Logitech Harmony 900.
This universal remote has several key features that can make operating all the components in your home theater system easier, including: Wireless Operation via either Infrared or RF Technology, remote code upgradeable via access to continually updated internet-based database, learning capability, control for up to 15 devices, and built-in touchscreen, as well as backlit buttons for execution of main activities and device control. The Harmony 900 also comes with an RF Receiver with three IR blasters (if using the RF remote option), rechargeable battery, and charging cradle. Also, a USB cable and PC/MAC interface software are also included.
You will find that the Harmony 900, with a suggested price of $349.99 (Compare Prices), is more expensive that many universal remotes, but is very versatile, and a lot less expensive than a custom installed remote control system. It is definitely worth checking out.