To answer your second question first, your model year of car should have two O2 sensors - one after the exhaust manifold and just before the catalyst, and one immediately after the catalyst.
Your first O2 sensor should not test the emissions from one particular cylinder/exhaust runner; it should be located in a spot just after where all the pipes converge i.e. in a 4-2-1 header setup, the O2 sensor should be after pipe "1". Have a look at the stock SVT exhaust set up.
If you are converting from a stock Zetec manifold, it is a simple case of extending the O2 sensor wiring harness to reach the new sensor location further downstream. Ford (and others) sell an extension for this purpose.