what are the tools and procedures to establish the Web Application development department in a company?

This is an open ended question. I would say the same way you create any department there is nothing special about a dev team. i.e. create an AD group 'development team' and add users to this group. In System Center or other management set up application installs that are specific for this group.  Set up access controls for specific shares applicable to the developers group.

I'm with David Johnson. This question requires far more clarity.

You'll have one general dev considerations.

Choose whether code developed will run in a Linux or Windows runtime environment.

Since you're tags contain .NET likely you're targeting your code to run on Windows.

There is no right/wrong answer, only considerations of long term time/cost of development + enhancement + maintenance.

Likely you'll just follow David Johnson's suggestion or provide far more detail in your question.