While installing DNN into IIS7 in production environment, Certain assemblies are not getting added dynamically - It asks for changes in Local registry... Please help

1)In IIS7 when i deploy the DNN web site i am getting some error saying that xyz***xyz.dll cannot be added dynamically for I used a custom built assembly to be referred in the Business layer escpecially i have used them in the controller classes when i add the custom modules.
2) Also the IIS is asking me to edit the registry entry , but if i do so i doubt whether the issue will be solved?
3) Since i was getting such error i deployed the DNN web site as a web application in Default web site and the site was working fine without any issue
4) But our requirement is to deploy the site as a main site and not as a sub-site or web application under a parent site.

Please kindly help me in this regard