First of all, on the Harmony remotes X-10 IR543 is considered as one single device regardless of what is connected to them (as akirby said). There are two problems you will run into.

One is that the IR543 can only operate the "A" commands. I think you would be better off getting the IR543AH which allows you to control devices within all of the 'letters'. That way you can setup every room under a different 'letter' and control them independently. A in your theater, B in your living room, c in the bedroom, d in the kitchen, etc. Otherwise, you may be limited by the number of devices that can be controlled by the X10 controller (20 per letter). Plus, if you have a different letter for each room you can utilize the ALL OFF command to shut off all of the lights, switches and outlets in that part of the house. If you are stuck with only A commands you will have to independently turn off each cluster of lights one at a time.

The other problem with harmony remotes is that you cannot setup true macros. Everything is activity based and activities cannot be run independently of whatever else you are doing. In other words, you couldn't run a "turn on kitchen lights" activity while watching TV because the remote would then power off the TV activitiy devices and then turn on the kitchen lights. And controlling the devices manually is a pain since each X10 command is really made up of 3 individual command and this is not ideal for X10 usage (you have to select the device code 'A', then the device number '4', then the command to send "off"). It works for me because I only use X10 in my theater and I can setup the lighting to come on as part of the startup activity. But in order to control lights independently it requires pressing a series of buttons. Not exactly ideal for whole house control.

You would be much better off with a remote that allows you to program your own macros, or a second remote that would be used for lighting.