net multi site VS blog registration

heres a quick over view on what I'm trying to do.

have a main site template- via New blog template.
create multi sties that run as their own site regarding the eshop shopping cart, each multi store will be on a sub domain.

I also have an affiliate program running, were admins have the option to sell multi sites. my question in:
When a new multi site is set up, does it matter if I create it via the superadmin dashboard? or can I have my affiliates create new sties, that work separately of the main site, via the "blog registration" option under the affiliates options tab?
I need the content, plugins, shopping cart to work on any new sites created, and also the tracking for which site makes sales etc.