I'll give this one a shot.
Emulation supports up to 48 fixtures, but with sub-fixtures. Sub fixtures are most commonly multi-channel dimmer packs. So you could have 48 quantity eight channel dimmer packs and use 384 dmx channels. That would work just fine.
The only time that you interact with the fixtures and or sub-fixtures directly is when you are working in the programming window to create a "look". Once you have your look set the way you want it, you hit the record button and select either a playback fader or button to assign that look to a playback. Playback faders are useful when you know that manual dimming will be necessary. Otherwise, use a playback button on the top.
Most users (including myself) only interact with playbacks during a show. It is much quicker this way. Playbacks have cuelists assigned to them. A cuelist can have as many steps as you like in it, and will behave however you tell it to.
As far as the midicon goes, it is a very flexible piece. The default midimap is very useful, but many users customize it to fit their needs. It works along side with the 8 playbacks per bank, 8 banks.
When you "grab" a fader, you can program it to start a playback fader, or dim one that is already running. To directly adjust the dimmer of a fixture, you would select the sub-fixture, then click on the beam button in the programming window, then adjust the vertical fader for this. Like I said though, this is usually only done during the programming process, not during a show.
To directly answer your question, you most likely wouldn't ever run a show from the subs, rather playback or "go" buttons / faders".
I hope this helps.
Michael Moore
Intense Sound & Lighting LLC
IntenseSL.com