.... I am not sure I understand. Are you using Visual Studio to create your applications? If you are, there is no need to upload your source files, just your aspx pages and the compiled .dll, effectively closing your code to prying eyes.
Do you own the boxes your site is hosted on or are they shared servers? This makes a big difference because if you own the boxes and just have them at a data center, then that is a huge problem if one of their admins are getting on your box without your permission.
If you are on a shared box, meaning the hosting company owns the box, there is nothing you can do about it really. THEY own the server and are the administrators of that box and can do anything they wish really. Also, if you are using a SQL Server that, again, is on a box they own they do not need to go through your code to get your password and such...they have admistrator rights to the entire box and hence the SQL Server.
I will only tell you how to do it, not do it for you.
Unless, of course, you want to hire me to do work for you.
Read this if you want to know how to get a correct reply for your question:
^^Took that from planoie's profile^^
^^Modified text taken from gbianchi profile^^