How to refer to a method from a workshop in a conference paper?
I think you are mixing up a few different definitions of "count" here.


Workshop papers typically "count" very little on your CV. That is, having a few workshop papers will not make you graduate much sooner, and they are pretty much useless when you start looking for e.g., a tenure track position.
Workshop papers, but only those with no formal proceedings, don't "count" as publications. That is, you can hand in the same material again at a conference or journal without being accused of self-plagiarism. The workshop paper on the website of the workshop is basically a preprint. Hence, formally, the work is still unpublished and you can submit it wherever you want.
Workshop papers, no matter if they appeared in formal proceedings or not, can and should be cited. Clearly, if you use this citation to, e.g., support the validity of a statement, this carries less weight if the cited source is a workshop paper than if it is a well-known journal. However, if you want to apply method A, which you have already presented in a workshop, it seems correct to cite the workshop paper. Note that you will still need to describe the method, as you cannot assume the reader of your conference paper to go back and read the workshop paper first.