ASP.NET WebSite Publishing vs. Copying?

I have faced a lot of issues with Publishing like when you need to make small changes on the code, sometimes the generated DLL file (the dll file for example of default.aspx.CS when published) cannot be recognized by IIS saying the codebehind is wrong or something. Sorry for not remembering the exact error message. I am hoping you know what I mean at this point.

Schedule a job in hosted web server

Can some one give me a best way to implement a daily job with .NET technology.
I have an asp.net application with the sqlserver database hosted in shared hosting, GODaddy in my instance.
My application is used to add / change the data in the database which is performing quite fairly at this time.
I got a new requirement to send some email alerts daily based on some data criteria that were stored in the database.