Digistras:
How do you intend to distribute the certificates?
If you were hoping enrolment would occur from the device, you are unfortunately out of luck with jscep. Currently, jscep does not work on Android devices. There is an open issue for a compatible version:
http://code.google.com/p/jscep/issues/detail?id=64
If you are going to build a client application to perform enrolments and then manually install the device certificates, jscep will be fine.
To address your specific questions:
1) No. You have to generate the initial request in your code and then provide it to the jscep client. See the jscep examples/FAQ pages.
2) This is registry setting on the NDES server, not a jscep option. See the NDES documentation.
3) Again, this is a setting on the NDES server. You need to configure your NDES server to fulfil requests using the Sub CA, rather than the Root CA. See the NDES documentation.
-- Ryan Schipper