So, thanks for the more in-depth info. First a few notes on general level, then a funny little introduction to get you started on patching.
Well, routing audio and midi (both internally and externally) doesn't get much more versatile than Usine.
My example: I have a MPC1000 slaving to Usine succesfully (haven't tried the other way) - and although i had perfect sync in Live for instance aswell I didn't have enough options; if the Live sequencer was running, so was the MPC etc. What I have in Usine is MPC receiving the midi clock from Usine all the time, but the MPC is independent. Only when Usine sees that the Play / Play Start was pressed on the MPC does it start the MPC on the next bar 1 beat 1 etc. Similar customized setups are endless. You can have eight different devices/midi ports both inwards and outwards from Usine plus each device can of course be sending receiving many midi channels. You can route anything to anywhere.
Just a warning: To get to where you want to be with your workspace will take A LOT OF WORK for a newbie. We are programming, after all. But the journey is pretty. And we are here to help.
The sampler is the source module for .WAV loops, the Piano Roll is for Midi loops. You can divide your elements into patches (many patches per track) and/or tracks (a total of 16 tracks with many patches in Usine Pro) as you find best.
You can either play with Quantize options for timing certain triggers or controls (found by right-clicking it) - this hasn't always seemed to do it's job perfectly though. Don't know the current status.
For Scenes - as far as I understand the term - I would opt to have a look at the conductor. In the conductor you can store a snapshot of the state of pretty much everything in the workspace, including master tempo. So probably you might end up with one (or perhaps several) conductor snapshots per song or for different parts of songs.
Very soon after you get into creating patches you will want to start to work on building an interface for your patches either in the Global Interface Builder or the Local Interface Builders. Even if you use controllers to control parameters it's still good to get into arranging the controls and displays nicely.
NOTE:
I recently noticed my MPC sync / control patch didn't work in versions higher that 3.63. Mind you, I haven't yet downloaded and tried anything above 3.65. I was planning to look into this in the next couple of days and find out what's up.
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Just a tour of simple examples to get you started with the sampler module:
In an empty track and patch add a Sampler. Ctrl-drag and release from the out pin(s), you will have the sound routed to the outputs. Double-clicking the sampler will open the file list. Add some sample/loop you want to play with. Now look at the sync mode of the sampler module. It's set to loop. If you have your audio engine running this means the sample should already be playing and looping. It's not looping in any relation to the timebase though.
Let's change the sync mode to Play button. The sound will stop. Now ctrl-drag and release from the play inlet of the sampler module. You will end up with a play button which you can find in the control panel of the patch. Now when you play that button the sample will play, on your command, once. Now right-click that button and select Quantize Bar. When you next press the button, it will wait for beat 1 of the next bar and play the sample once. Also by right-clicking the button you can do a midi learn for that interface element (if you have your control surface selected and active in the setup). You can also do a key learn and use the computer keyboard for triggering the button.
Okay select the play button in the patch and delete it. Add a master synchronisation (hi cpu) to the patch. This is the module with all the timebase and synchro stuff. The outlets named "[something] led" give a trigger at certain moments. Try connecting the cyc led outlet to the play inlet of the sampler. Now it's triggering the sampler on every first beat of a bar.
Next, delete the Master Synchro module and add a Switch (interface design), a 0to1 (events control) and a 1to0 (events control).
The sampler's sync mode still being "play button" let's try something else:
Do the following connections:
Switch.out > in.0to1
Switch.out > in.1to0
0to1.out > play.Sampler
1to0.out > stop.Sampler
Make a key learn on the switch. Then right-clicking on the Switch select Remote mode toggle. This means when you press the assigned key on the keyboard for the first time it switches on and when you press the second time it switches off. The moment it switches on (0to1) is routed to trigger the play of the sampler. The moment the switch goes off (1to0) triggers the stop. Now it will only play for as long as the switch is on.
One final little example of some event control patching:
Leave the Switch but delete the connection cable leading to the sampler. Also change the Remote mode of the switch to Absolute. Add the following modules: a 0to1 (events control), a Pass Event Flow (events control) and a And (math/logical). Now make the following connections:
Switch.out > in.0to1
Switch.out > A.And
Sampler.stopplay > B.And
Sampler.stopplay > pass.PassEventFlow
And.out > in.PassEventFlow
0to1.out > play.Sampler
out.PassEventFlow > play.Sampler
In this case it will be re-triggering the loop as long as you keep the assigned key pressed. A break down of what we just did: When switch goes on (0to1) it triggers play. When sample reaches end (stopplay) it re-triggers play IF the switch is still on (1) at the time the stopplay trigger hits. I.e. IF switch is TRUE and stopplay is TRUE then LET PASS the stopplay trigger into the play inlet. Try it out.
That's just some sort of quick introduction in the ways to build towards different goals. A scratch of the surface. Now, try building something according to how you want it to work and when you're lost we will help you. Ask any question, don't worry whether it's a "stupid question" or not.
We'll take it from here

Have fun, be patient.
antwan