I just finished setting up my HTPC that uses the exact setup you are looking for: XBMC for all media and WMC for TV and recording and also using a Harmony One remote.
What I did is setup three activities on my remote:
2. Live TV
3. Recorded TV
I pinned XBMC to the start bar so by using Win+1 I can launch the app.
In the activity setup on the remote, I have the following (going by memory as I don't have it in front of me)
XBMC: Send Win+1 command (I think that is using the SE device)
Live TV: Send "Live TV" command (using MCE remote device)
Recorded TV: Send "Record TV" command (using MCE remote device)
One issue you might encounter is related to sound.
WMC, as a Microsoft app, hijacks the sound so that when switching over from WMC to XBMC you still hear the sounds from WMC (unless you close the app).
If you mute WMC, it'll mute your whole PC.
For my needs, I wanted both WMC and XBMC to always run and not launch on demand (WAF).
This can fixed pretty easy, but it does require a bit overhead.
This is what I did:
1. Install the NirCMD tool (http://www.nirsoft.net/utils/nircmd.html
2. Create two batch scripts:
a. WMCSound with the following two commands:
nircmd setappvolume xbmc.exe 0 (sets the volume for XBMC to 0)
nircmd setappvolume ehshell.exe 50 (sets the volume for WMC to 50)
b XBMCSound (same as above but WMC to 0 and XBMC to 50)
3. Pinned both scripts to the windows bar
4. Change the activities in the remote to first execute the script and then run the app.
With XBMC is was simple: Command will be first Win+2 and then Win+1.
With Live TV/Record TV it is a bit trickier as I am using the MCE remote built in commands and the activity requires you to select an input source. What I did is to create a new input called NOOP that does nothing and that is the first command that the Live TV/ Record TV executes. Then do the Win+3 to run the script and then the Live TV/Record TV MCE command.
This works almost perfectly and the only issue is that when switching between apps you see a glimpse of the OS and batch window. It's very quick and passes the WAF, so not a biggie, but still annoys me.
Hope this helps and let me know if you have any more questions.
BTW, this my first HTPC and first time I'm using WMC and XBMC (was using Boxee Box until now), so I don't know a lot more then I know.