(1) use the USB UIRT. You can get them here..
http://www.usbuirt.com/We have a device template for a standard Windows MCE remote that will work out of the box, and you can create other device templates to work with other remotes.
This device also has IR learning and blasting capability so you can learn the remotes of other AV devices and control them.
Keep in mind too, that LinuxMCE can be controlled by a huge variety of devices, most of them running Orbiter, such as:
* Tablets
* PDAs
* Cell phones
* Cisco 7970 IP phones
* web page display capable devices
Please read the wiki article on Orbiters, for more information.
Also:
(2) you may be confused about the terminology of a core. There is only one "Core" in a house, but there are multiple Media Directors and Orbiters. Any peripherals attached to the core or media directors are shared house wide to the other devices on the network. This system is meant to be the center of your home. Design your network as such.
-Thom