Still not quite sure what you are getting at/asking. That we use cabinet emulated out puts and plug straight into:
- a mixer (and then into the I/O) or
- the digital I/O device (in my case digidesign digi 001 (8 in 8 out A/D D/A)) or
- the computers sound card input (not my preference as they're not generally that good although you can buy decent sound cards if you want to spend the $s' and latency (syncing between the audio tracks and what you hear to play back to) becomes a bigger issue or
- into DAW inputs (same as a computer except dedicated to the task)
If I micked up the speakers the microphones would plug into the above in much the same way except for input levels (line vs mic) so I'm just cutting out the need for a power amp and speakers and mics (not to mention outside noise spill, traffic etc into the mics). If the cabinet emulation of my MP2 wasn't as good as it is, I would mic the speakers instead and/or if I was after a particular sound (amp/speaker/mic combination) again I'd go to the trouble of plugging it all in. So there is no real difference on the input side (apart from signal levels which you can adjust) between plugging the preamp in directly or micing the speakers.
However, (and maybe this is what you are getting at ??), if you use the computers sound card to record and monitor the sound, there will be latency issues when you want to play back a track(s) and record another track or overdub on a track. It takes time for the playback to be processed by the sound card and then get to your ears so additional tracks you play/record (which you hear in real time as you play them) will be out of synch with the earlier track(s) by the amount of delay (latency) introduced by the particular sound card. The sound card/modules included in more recent mother boards (it used to be that the sound card was separate) are usually pretty bad with quite long latency (as were the older sound cards). The quality of their AD/DA conversion is better than it used to be but stll not that great (depending how pedantic/fussy you are) which is one of the reasons to buy separate dedicated I/O devices (which also generally support more simultaneous inputs and outputs (eg 8, 16, 24 etc) and have much less latency (they all have some latency)). With 8 inputs you can do a basic live recording (eg bass, electric drum kit, guitar, keyboard, guide vocal) all at the same time (with no latency :-) ) and apart from the guide vocal (I use an SM58 to reduce spill) all the other instruments are direct and not subject to spill so you can get a reasonable result at home and the live tracks are all in synch with each other because they were recorded at the same time. New tracks and overdubs are still an issue.
On the other hand, (as raved above), if you use a separate analogue mixer for inputs and "ALL" monitoring, all the sounds you hear come from the mixer (both playback and new inputs) at the same time and the sound card I/O latency issue goes away.
When you combine audio and video streams to make a clip, they can be out of synch. In VLC for example, there are options for delaying one to the other to get them back in synch (it's fiddly but it works). Audio and video files (eg .wav, .mp3, .flv, .vob etc) are basically a "bucket" within which are stored the encoded audio and video bit streams. When you play the file, different video and audio codecs are used to play the appropriate stream.
Not sure if all this helps as I'm sill not quite sure what you mean ? What are you trying to do where synching is an issue ??