You don't have to add them specifically as Midi Instruments as they don't have any physical outs as say a MiniBrute would have, or a controller keyboard, Beatstep etc.
They are soft synths so only exist as long as you have a computer. What I tend to do is to open all the standalone apps up that I want to play, Say the Mini V, Prophet and SEM. In the top window of each standalone app you'll see a midi channel, starting with 'All'
I assign the Mini V to Ch 1, the Prophet to 2 and the SEM to 3. My 2 keyboards are then programmed to communicate with each instrument specifically per each channel. I have a split on one where for example from C0 to C2 I use the bass of the Mg and from C2 upwards use the prophet. I have an Arturia laboratory 61 and each patch is set up with the Arturia midi centre and sent to the keyboard. This way I can switch presets with the preset keys on the 61. My other keyboard is an M Audio which I set up in a similar way.
Do you have analog lab in your collection. I have used this from time to time, setting up patches but sometimes it hasn't been very reliable so I switch back to each separate app.
You could run them in a DAW, ableton is fine for things like that but depends on how much you want to run and how fast your computer is.
There is also the Receptor, depending on your budget, but I've worked with a few guys who use these. They essentially run plug ins from dedicated hardware and can be used to off load plug ins so that your CPU no longer has to do any heavy lifting. These are rock solid.
Cheers, Stuart
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