Note: First thing is to check with the owner of the server, as they often will provide you an FTP connection and will take care of configuring IIS.
If you want to add security, make a keyfile and sign your assemblies and consider running Dotfuscator on your dlls, the community edition is included in Visual Studio. Here is an earlier question where I've put more info on Dotfuscator.
If you have to do the deployment yourself, here's a few things to consider.
- XCopy (easy)
- MSI (have to create a setup program, you can do this easily in Visual Studio)
There is no security advantage in deploying using Visual Studio, but you can use Visual Studio to create a small setup program. One thing you want to make sure for security is DO NOT deploy any .cs files. Prepare your files, you should compile in Release mode, make sure debug is not enabled in your config file, keep your bin and it's dll, also the aspx, asmx, ascx, svc, css, js, and config files.
- XCopy: Install a small FTP server, or use one your company alreayd has, this will allow you to get your files once you are logged into the target machine. You should be able to get an administrator account for the target machine, just ask the sysadmin of the domain, then log on using remote desktop, got to your ftp site, and download your files. Open IIS on the target machine, create a virtual directory and a pool. Copy your files to the location, configure your connection string to your DB if you use one, then test your website.
- MSI: same process as above, except the setup will create the virtual directory and pool for you.
Here is extra info on best practices from the official ASP.Net website.