Also, search within the automap app for other options. I think it works with different stuff for different things: for example, there's a thing there called "automap hub" which is their own hay of handling midi info for software, through the automap app, then there's rather more conventional midi also. I think this last part is pretty much reserved for the user button and templates you build. They thought this out primarly for hardware's direct control, with the templates you can build with the editor, but not only that. I have the little nocturn and use it to control traktor, the dj software from Native Instruments sometimes at home, so that isn't really compatible with standard automap and I had to set a template for it that's saved in the user templates. By pressing user I can choose my traktor template any given time.
The extra convenience of using usb to connect it, like I said, is that you get to choose from controlling software or hardware by simply pressing the "automap" button on the controller, instead of having to plug in and out cabbles for each, which is a time saver and much more convenient.
But I think you'd be happy to, say, select two of your synthesizers to receive info from the computer, to play notes you have written there (either using Reaper's writting tools or recorded keyboard action of course) and record the audio outputs of those. If you use the "throughs" on this channels or the devices themselves, you can extend this functionality to all your collection of hardware. You'll probably get more lag the longer the chain goes, I think. But if you happen to have some "delay compensation" feature on Reaper, it can compare the notes timming and the audio and correct this automatically for you.
If however this becomes an issue, I think a simple and cheap midi bridge device with some clock inside it (the remote can send clock info, granted!! another useful thing for hardware people) would allow you to sync everything up. But don't take my word for it, my collection of hardware isn't anywhere as big as yours. I know for a fact that RME has very good clocks, but again, this is quite expensive stuff...
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