Lets first differentiate between RELIGIOUS BELIEFS, RELIGION and RELIGIOUS INSTITUTIONS. Each requires a different approach.
One can describe these three concepts in chronological order as follows:
At the base are the individual needs as explained at length by the Embryonic and Parental Shell Theory. These cause the urge for RELIGIOUS BELIEFS.
Sets of religious beliefs (including those beliefs that necessitate actions such as offerings and prayer sessions) accepted amongst groups of people are RELIGIONS.
Next, RELIGIOUS INSTITUTIONS basically came about to help perform the executive aspects of religion, such as the organization of ceremonial services. In this respect they are no more good or evil than religion itself.
However, throughout history and amongst the nations the basic human needs have always been an extremely efficient tool in the hands of those that strove to obtain power, or to retain it.

Religion in this respect is no different from any other basic needs such as food or sex.
Anyone in charge of an organization that controls these matters, being able to grant or withhold, allow or prohibit, can extend almost unlimited power over the people in need.
However in the case of religion the power can be even greater and certainly more dangerous.
First, the person in charge is affiliated and associated with the Divine, and therefore some of the divine holiness rubs off on him too, formally or informally. This only increases his power. He can demand extreme subordination and will be granted his demands.
Secondly, since the religious persons beliefs are vital to his inner feeling of security and well-being as explained above, his emotions concerning these beliefs can be very easily manipulated in order to stimulate him to act in a manner that advances the interests of the religious leader or his patrons (kings, presidents etc.)

Therefore, the tactics to be employed by atheists when engaging in discussions with theists (in case the atheist wishes to take an active stand, which is of course an individual decision) should differ according to the circumstances of the interaction:
RELIGIOUS FEELINGS:
When dealing with an individual expressing inner feelings and emotions of religious nature, the psychological theory laid out on this site can be applied to explain to him a very plausible alternative origin for his feelings.
RELIGION:
When dealing with an individual who mainly stresses axioms and truths as presented by his religion, his statements should be countered with mainly philosophical logical arguments, though the psychological basis underlying his own beliefs may also be mentioned. The philosophical negation of religion is not dealt with on this Website, but is extensively elaborated on at many atheist websites and newsgroups.
RELIGIOUS INSTITUTIONS:
When dealing with persons clearly representing the religious establishment, one should avoid focusing the discussion on matters of theological nature since usually the matters at stake are those concerning influence, power and other non-religious interests. The discussion should therefore focus on issues such as freedom of though and speech in a democratic society and the legitimacy of atheists voicing and advancing their views as openly as any religious person.