for diving in manado, u got a lot of options actually.
if u are more concern about safety and good boat, then ecodiver is better for you, they only dive 3 times/day max.
I dived with them, and really satisfied in term of professionalism and their boats are nice..
in the other hand if u go with other dive center, such as NDC then u got urself a cheaper rate, but boats are not as nice as ecodivers' and also rooms are below tasik ria (ecodiver), however just last year some NDC rooms had been renovated and they are as good as new, but just few of them.
In my experience, NDC guides are more 'fun' and providing, i dived with them 4-5 times a day.
If u decide to go with one of the dive center, u can also ask for them to arrange ur diving in lembeh, no need to change dive center...
this is my opinion, hopefully helping bit... IMHO...
Cheers,
Bodiver