This question has been asked and answered more times than I can count. ( How can I bill within an application )
In addition to that information, you should also check out:
Which talks specifically about a MS RMS approach.
I believe you can setup RMS to import records from a SQL database. which I'd look into, because I think that it will be a lot easier for you to process the transactions in .NET directly through your gateway of choice, and batch the resulting records for import into the RMS system.
This company claims to offer a product that might make your life easier, but i've never used it, or heard about it before now:
Ditto with this one:
Otherwise, regarding iPhone <--> Server, I'd suggest you check out setting up a WCF service which uses JSON. or look into the objective c soap client proxy generators. but, honestly, JSON is just much much easier to deal with on the iPhone.
Copy of my answer from the other thread:
There are lots of ways to go about setting up e-commerce sites;
If you don't have any experience whatsoever, and don't want to get into anything "complicated", i would suggest going with a customizable web "storefront" hosted by someone else, pre-integrated with credit card processing, etc. There are tons of options for these online. Just search google for "web storefront". Yahoo! even has such a service:
Going beyond that, It's pretty easy to integrate with someone like PayPal. They have all sorts of options from the most basic (use a link to send someone to their site with query string parameters to let paypal know what the user wanted to buy):
Beyond that level, you will need to signup for a merchant account, or other similar sort of service, like the one offered by authorize.net (who I like):
There are components you can buy for most major web development platforms like .NET, JSP, etc. Perfect example is dotnetcart. These components provide out-of-the-box, easy-to-setup integrations with major CC processing companies, as well as out-of-the-box shopping cart implementations:
Finally, most merchant services / payment gateways provide web services for direct integration.
PS.) Never ever ever store CC numbers ; )