It is best to keep the hours in separate logbook columns, but not necessarily a separate logbook. For example, if you have a conventional PPL logbook there's probably a couple of "multi-engine" columns in there - just stick a label on the headings changing "multi-engine" to "microlight" and you're fine.
You'll need microlight differences training (with a microlight instructor) for legal reasons but presumably you can do that before you've got your PPL(SEP), and you could pay an instructor to do that in the aircraft you are buying a share in so long as the aircraft is type approved (often called factory built), although they can't sign that off until you've got your PPL(SEP). One would assume your syndicate and insurance company would be happy with an instructor instead of one of them.
That said, I'm not a licencing expert, just somebody with experience and a collection of licences. You'd do well to phone 01869-338888 during the week and ask to speak to Roy Hart; Roy is BMAA's licencing guru and can give you chapter and verse.
G