I've been at Apnea Total 1½ year ago. Did beginner course+adv. Great school, nice people, nice diving. However they are not affiliated with any certification "school" (AIDA, SSI etc.). They are what they are = great place, people and diving. They can give you certification, but it doesn't relate to other than the place itself. That can be ok, but if you need a specific certification from one of the bigger schools, to get a job, it might be a problem. Also they don't use any course books (at least when I was there at my courses). We got a password for writting material on their website after the course). My impression is, that they run the courses less formal and more easygoing, in the spirit of the "Zen of freediving..."
Been at Blue Immersion in Dahab last month for some deep training. Great school, people and diving/training. Never done courses, but watch other people taking them. It is much more school-like. Haven't been at the place in Koh Tao. But since they merged, they are probably doing things similarly now. So as far as I can tell, they do both AIDA and SSI courses (both of wich are well known world wide, and you can "change school" inbetween). They have course books and run things much more formal and proffesional/according to course material, that's my impression... I have no idea about what the school everyday "feel" is like... Linda from Dahab is currently there for a few months...
As much as I loved the place and people at Apnea Total, given that you are allready AIDA***, keeping that line of learning might have benefits for now... for an instructor course, AIDA or SSI certification is probably also the more safe choice investment-vice, if you need a job afterwards.... However, that is only a qualified guess... And both will certainly produce good instructors, that's my impression... If you're not in need of a specific certification, like if you start your own school (or if Apnea Total cert. is accepted elsewhere), and you are the more chilled kind of guy, Apnea Total might be more suitable for some...
These are my subjective impressions...
Send both an email, explain your wishes and motiavation for the course, and see what they say...