Roger, am I right in assuming your Logic version is pre-10.7?
If so, have you switched on "Auto demix by channel if multiitrack recording", in the File/Project Settings/Recording settings window? That will ensure that once you stop recording your multiple MIDI streams, Logic will atomatically separate the various recorded MIDI tracks such that each single-channel part is placed on the relevant template track. And if that has been activated, have you ensured that the channels on which your various MIDI controllers transmit to Logic's Sequencer input, match the various VEP template channel numbers you've chosen to be played by your MIDI controllers?
I've often seen other Logic users setting up Transformers in the Environment to make it more convenient to assign the required track-channel numbers to inbound MIDI controller data; and that's what I've always done too. But if that's not a preferred option for you, then you'll have to assign the internal MIDI channel number on each of your MIDI Controllers, in order to match the channel numbers in your template that you wish to be played and recorded together.
I've done a quick test using one of VSL's Beta AU3 templates with Logic 10.4.8, just to confirm that Logic's auto-demixing feature works as it should with AU3. And it does. See attached screen grab of my test. I ran the test specifically because I couldn't remember if the auto-demix facility works across VEP port boundaries; but as you can see from the test results, it does. It appears that MIDI channel numbers 1 to 16 are all that Logic needs for the auto-demix function, regardless of MIDI input ports or track AU3 output ports.
In the test I made 5 separate recording passes, playing in random garbage on 4 different MIDI controllers in every pass, on input MIDI channels 1, 2, 3 and 4. In each recording pass the 4 MIDI controllers recorded into a different selection of tracks in the VSL template, but keeping to (for convenience) template channels 1, 2, 3 and 4 in every pass. The last 2 passes each covered more than one VEP port. When each pass ended, the recorded MIDI channels were separated and placed correctly in their individual tracks by Auto De-mix, as seen in the screen shot.