Aida-
I hope I'm addressing your question correctly. I'm not an expert, but I've rubbed shoulders with this issue. At least with medical devices, it depends on the risk-based classification of the equipment.
Per the Medical Device Directive, Class 1 non-sterile/non-measuring devices can be 'self-declared' (see Annex VII)and the CE mark applied without witnessed testing or quality system registration. You do need to have documented testing, technical files, etc. available upon request.
For Class 2a or higher, you need both a Declaration of Conformity and either registration to a recognized quality system (read ISO 900x) or witnessed (and expensive) testing.
This is a narrowly focused response to a very big question and all I can offer based on experience.
This is an area where a good consultant would be worth their weight in platinum!
Best of luck with this one.
Alf