You can very well register your institute as a Proprietorship, pvt ltd, or a ltd firm.... or society etc... It does not matter what kind of registeration have been done but you can issue a certificate in all kind of registerations... the affiliation is a different thing, it is like working for somebody else or on some other institute's behalf... it does not matter..
only for providing degree courses it is necessary that you should have the institute approved by AICTE, otherwise in any other certificate coures you are just needed to be registered anyhow in any form.... In our Indian culture our students call this registeration as "manyata praapt" for institutes and for any other establishment as "registered"...
It may cost you around 2000 to 2500 (4000-5000 if get done by someone else) rupees only. The proprietorship registeration is can be done through a CS (company secretary) and is very easy... For pvt ltd or Ltd registeration you should go to the registrar of companies, it may cost around 7000 (13-14 thousands if get done by someone else)...
For institute you must possess the genuine windows or any other softwares... You must get your registeration number printed on your certificates, and you must provide a list of students who have passed out on any of your websites for authentication purposes..