Development environment : ASP.NET 2.0 , Visual studio 2005

I am looking for a good method for deploying my ASP.NET application. I have used "Publish website" feature with "Allow site to updatable" checkbox checked. This worked correctly, but I am facing some problem in updating the site after deploying. I did the change in local machine and used the "Publish website" again, but it changed all assemblies names (assemblies which starts with app_web).

There is another option to avoid this by checking "Use fixed assembly names" checkbox. But it will generate each assembly for each page, so I will have many DLLs in my bin directory. Is there any performance impact for this method ? Or do I need to use aspnet_merge.exe and merge assemblies ? I need to update this site regularly. Please suggest a good method.

Thanks