Matthew, I'm really not clear on what some of these terms mean or what you need.
"connected over IIS to their database" - Is this a DevForce application connected to a BOS running under IIS?
"our web based server" - Is this a web service?
"if we could have multiple IIS connections ..." - ??
Although I don't understand the use case, here are a few things to look at which may help:
- a custom DataSourceKeyResolver, which would allow you to hide connection strings from the user, and possibly encrypt the connection string (although you would be responsible for decrypting it)
- use of the PersistenceServiceOption flag when creating the PersistenceManager to control whether it will use the BOS or not
- directly calling the web service from your application w/o DevForce involvement