Do atheists ever engage in circular reasoning? They most certainly do and they do it quite often.
One of the most common claims of the “New Atheists” is that science proves religion wrong. Yet as the New Atheists agree, science is (currently) defined in such a way that it cannot support religion or point to God. If any scientific theory does point to God, it is immediately dismissed as “pseudoscience.” So what many atheists are actually claiming is that a method, which can only support their worldview, proves that their worldview is correct. That certainly sounds like a circular argument.
To be sure, it is perfectly legitimate to consider scientific (i.e. empirical) evidence when evaluating religious truth claims. However, that evidence needs to be lifted out of the realm of science and considered within the realm of philosophy. It is only in philosophy that one can follow the evidence wherever it leads.