If you look in the web.config file for your application, you should have a section called system.web. Within that there is a membership element with a list of providers. You should be able to add your provider and set a default provider there. Once your membership provider is registered in this way, you should be able to select it as a default for that application from IIS as well.
<system.web>
...
<membership defaultProvider="MyMembershipProvider"
userIsOnlineTimeWindow="15">
<providers>
<add name="MyMembershipProvider"
type="Common.Auth.MyMembershipProvider, Common"
connectionStringName="MyAuthDBConnectionString"
enablePasswordRetrieval="true"
enablePasswordReset="true"
requiresQuestionAndAnswer="true"
writeExceptionsToEventLog="false" />
</providers>
</membership>
...
</system.web>
The providers element allows you to register multiple providers to choose from. Another feature is that you can clear out membership providers registered in other configuration files on the machine. This can make configuring your application less error prone later on. To do so, add the <clear/> element before the first membership provider (the <add/> element) in the list.
<system.web>
...
<membership defaultProvider="MembershipProvider1">
<providers>
<clear />
<add name="MembershipProvider1" ... />
<add name="MembershipProvider2" ... />
</providers>
</membership>
...
</system.web>
If you want to register the same provider with multiple web applications just using IIS Manager, you will need to put the assembly in the GAC and add the provider to one of the machine config files instead. This is usually more work for little benefit when deploying a single application.