The title of this question might be a bit clumsily phrased, but here\'s the situation:
I have a .NET web project deployed on my server.
It sounds like you need to take a look at a custom MSBuild script for deployment.
MSBuild does much more than just build solutions. You can also use it to copy files and update them, too. A good resource for tasks to do this is the MSBuild Community Tasks here.
You can then include the deployment of your background process alongside the deployment of the Web site deployment.
An alternative approach might be to use Windows Powershell with something like PSExec to remotely execute copy and update commands.
Both these kinds of approach can be automated very well with continuous integration servers such as Hudson. I have a build process that automatically monitors my source code repository, builds the program, deploys to a staging server, runs acceptance tests, then deploys to a preview box. I have another (manual) job that with one click deploys this preview version to live, minimising downtime and (usually) reducing errors from mistiped commands.