Hi Wen,
If I was tackling this Id have 3 certifications and one program for the courses you mention 12, 8, 3 & 1. So that would be 4 enrollment messages initially.
There's no need for anyone who isnt a newstart to be enrolled into any of these courses by the newstart program/certifications, in fact Id imagine it would make reporting easier if you used separate progs/certs.
cheers,
George.