The "configSource" supports only one config file, so you can't have multiple config files by default. This goes alose for the node in the web.config.
I suggest you try to do it programmatically You can use ServerManager class to get access to website configuration. You will probably need to add a reference to Microsoft.Web.Administration. Read your config files and add each rule mannually.
Something like this:
using (ServerManager serverManager = new ServerManager())
{
Configuration config = serverManager.GetWebConfiguration("Default Web Site");
ConfigurationSection rulesSection = config.GetSection("system.webServer/rewrite/rules");
ConfigurationElementCollection rulesCollection = rulesSection.GetCollection();
ConfigurationElement ruleElement = rulesCollection.CreateElement("rule");
ruleElement["name"] = @"rule";
ConfigurationElement matchElement = ruleElement.GetChildElement("match");
matchElement["url"] = @"foo\.htm";
ConfigurationElement actionElement = ruleElement.GetChildElement("action");
actionElement["type"] = @"Rewrite";
actionElement["url"] = @"bar.htm";
rulesCollection.Add(ruleElement);
serverManager.CommitChanges();
}
There is also another option but I haven't tried it myself. You can write your own custom rewrite provider for url rewrite module. Here is a walkthrough how to do it: Custom Rewrite Provider Walkthrough