Sorry I didn't get this out sooner. It's been a busy couple of days. Here are the steps to make a universal 32/64-bit FxPlug.
To make a universal FxPlug from an existing 32-bit FxPlug:
1) Open your existing FxPlug
2) In Xcode's Files and Groups pane, select the 32-bit target, right or control click on it, and choose "Duplicate"
3) Rename the Original to something appropriate (like <PluginName>32bit or whatever)
5) Create a new "Aggregate" style target by choosing "Aggregate" in the New Target dialog in Xcode. Switch to this target.
6) Make the 32-bit and 64-bit targets be dependencies of the Aggregate target
7) Add a "Run Script" build phase to the aggregate target and enter this as the text of the script, replacing <PLUG-IN_NAME> with the name of your plug-in:
# Remove the 32-bit variant if it exists or the next lipo call will fail
lipo ${BUILD_DIR}/${CONFIGURATION}/<PLUG-IN_NAME>.fxplug/Contents/MacOS/<PLUG-IN_NAME> -output ${BUILD_DIR}/${CONFIGURATION}/<PLUG-IN_NAME>.fxplug/Contents/MacOS/<PLUG-IN_NAME> -thin x86_64
# Add in the newly build 32-bit variant to the 64-bit variant
lipo ${BUILD_DIR}/${CONFIGURATION}/<PLUG-IN_NAME>.fxplug/Contents/MacOS/<PLUG-IN_NAME> ${BUILD_DIR}/${CONFIGURATION}/<PLUG-IN_NAME>32bit.fxplug/Contents/MacOS/<PLUG-IN_NAME>32bit -output ${BUILD_DIR}/${CONFIGURATION}/<PLUG-IN_NAME>.fxplug/Contents/MacOS/<PLUG-IN_NAME> -create
8) Build the Aggregate target and either copy the resulting FxPlug into the Plug-Ins folder or make a sym-link to the built binary as you normally would
Please try it out and let me know if it works for you. I suspect that there's some Xcode variable I could have set in step 7 so you don't have to type your plug-in's name 10 times, but I don't know it off the top of my head. Also, here's an example plug-in that shows it in action: