When it is recommended that cats be introduced the "right way" it does not mean all in one day. This process of introductions can take weeks, even sometimes months, to get it right. Doing it in one day is like not separating them at all. The idea of separation is to let them get used to the smells, sounds, and habits of the other cat(s) in the household. Then you can start doing a s l o w introduction by rubbing/exchanging scents for a few days, then exchanging the rooms. Let the new cat out into the rest of the house. Put the resident cat in the room the newbie was in. It takes quite some time to achieve this.
The website I've posted is excellent for showing how to introduce cats properly. This lady walks the walk. Please take the time to read it carefully. Until you do it would be a good idea to separate the cats again. This time to do it the right way.
http://www.squidoo.com/multi-cat-management