First of all, you'll want to obtain a copy of IRS Publication 1828, available online at the following link:
This will give you a lot of valuable information in connection with your dealings with the IRS.
As you know, the IRS considers Churches as automatically exempt under 501(c)(3). This status has it's roots in the US Constitution's provision of Separation of Church & State.
However, there are various reasons to obtain confirmation that any particular church qualifies for the exemption. As you know, that confirmation comes in the form of a letter from the IRS. This is the same letter that any 501(c)(3) organization receives once they file their application and it is approved.
To answer your initial questions, here's an excerpt from Publication 1828 referenced above:
Applying for Tax-Exempt Status
Employer Identification Number (EIN)
Every tax-exempt organization, including a church, should have an employer identification
number whether or not the organization has any employees. There are
many instances in which an EIN is necessary. For example, a church needs an EIN
when it opens a bank account, to be listed as a subordinate in a group ruling or if
it files returns with the IRS (for example, Forms W-2, 1099, 990-T).
An organization may obtain an EIN by filing Form SS-4, Application for Employer
Identification Number, according to its instructions.
If the organization is submitting:
IRS Form 1023, Application for Recognition of Exemption Under Section 501(c)(3) of
the Internal Revenue Code, Form SS-4 should be included with the application.