Thanks for everyone's suggestions - yes, I'm finding this confusing
The trigger wheel is set up as on a standard Ford - at least, I assume it is, since that's what the MegaJolt needed (I didn't fit the wheel myself). When I idle the engine with std dizzy + coil, the missing tooth is visible at about 10 degrees. Still not entirely sure what I should set 'TDC after trigger' to, but I'll fiddle with the settings until timing matches the VEMS advance value.
Had some trouble getting VEMS to fire the coil though (in that it wasn't firing at all) - having unplugged everything and come in for the evening, I've realised it was on 'Safe Mode', which it seems disables ignition & injection. How stupid do I feel?