Can't help you with the 1and1 question, sorry.
Regarding your three sites, I offer the following observations: DNN can work in the three subdirectories, but I think that you will run into problems if you install an upgrade on one subdirectory that updates a database table or two, which may well screw up one of your two other sites.
Another way, as you know, is to use the facilities of DNN to run these three sites with one codebase, one database and one IIS website, just changing host headers to ensure that IIS responds correctly. In the event of a problem with one of the sites that requires a database restore, your other two sites will be regressed too.
I started off this way, and it's a great way to save money and share modules, but...
if you are going to do this hosting commercially, in my view you should use one codebase/database/IIS node per website, or, if discussed with the customer, one codebase/database etc per customer. My reasons for doing it this way are that recovery is much more straightforward and one mistake (either by you or a customer) is not going to screw up another customer's system. Me, I do separate codebases etc for each customer, and for one customer in particular who is planning to have a lot of user interaction and input, there will be separate codebases/databases for both of his sites. Yes, it will cost you more to set up, but given that modules are generally very good value for money, any customer that isn't willing to pay such small amounts for the functionality and richness that the modules offer, probably isn't a customer that you want.
The module developers will be grateful to you too.
Sorry, went on a bit there, and probably none of it applies to your situation