Deployment and Updates

Question

I have finished writing an FTP application for my company. I am looking for the best way to deploy the application and provide updates. I have been looking at using ClickOnce deployment provided by Visual Studio. The problem that I am running into is that I don't like the fact that if you use ClickOnce you can not configure it to place an icon on the desktop and it does not create a program folder. I don't want to use MSI packages because it will be too complicated to get to all the needed users. The way I want it to work is that I can deploy the application to a web server and through some programmatic logic, have it check that server periodically for updates. If someone could point me in the right direction I would greatly appreciate it. Thanks