If a customer is running ecommerce then the the extra cost of a ssl certificate to run the https pages should not be too much of a burden for them. Also looks a litlle more professional than https://customername.someotherdomain.com.
For windows I think you have to use a wildcard certificate and assign a client a subdomain. This can be rather expensive.
The other way is to setup a secured domain with a normal certficate and give the customer an account as a folder under that domain.
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Hi you just setup a secure server maybe name abc.com
Setup a directory under it maybe yourclient, then give ftp to that directory, your client will be able to use https://www.abc.com/yourclient, you only need your own IP for the secure server, clients uses your cert.