VE Pro is essentially a multi-timbral instrument to the host, eg., Cubase in terms of routing. There is no mystery, you enable outputs in the F11 rack the same as you would anything that provides them to Cubase. Then in the Vienna Ens Pro instrument channel there are the subchannels representing those choices.
One thing I would suggest is having a reason for these choices. If at some point you need 'stems', ie., a separation of the mixdown of that instance, this is a concrete reason for more than one out. Or you may want a level control in Cubase in addition to the level you can automate of VE Pro's mixer so you make an output. But with the automation mapping and control you don't necessarily need to clutter Cubase.
It's a matter of how you want it organized. I like 4 outputs, maybe a couple more in a really involved setup, the master and three rather inclusive categories. Some really just need one stereo master output.
It's a host. You add the plugin eg., Kontakt or Play or Vienna Instruments to VEP, I don't know what the mystery is. Right-click and 'add plugin' or in the case of VSL's engines, 'add instrument (VI)' or 'add VI Pro' and there are key commands to do the same thing.
I remember when I started with virtual instruments and trying to suss things by reading. Just get in there, the interface is very intuitive, and do it.
There are these types of channels in VEP: instrument; bus, which the instrument can be sent to in order to be effected by its inserted effects, or assigned to so that everything in that bus effects it; and input. The latter functions for a couple of things; the basic one is this: If you assign outputs from eg. Kontakt, you input that from the menu of that Kontakt channel's outs. Or a bus is just a group, such as I have a whole flutes ensemble assigned to 'flutes' bus which give me a master level for the group.
I make a midi port for a family; similarly I make a (not-huge) multi in
Kontakt for like things and set outputs as needed for mixing. It's all
up to you and your idea of organization.
I don't think there is going to be much difference as to the loading times of channels using one or many viframes, other than the obvious time to start up the frame. It uses a little bit of cycles to use more than one vs one, so I think dozens of instances is not very useful. I do 2-4 typically for various reasons. I used to have to isolate Play. I isolate BFD2 because of a couple of bugs. I use some FX which are not 64-bit so there's an instance.