The measuring protocol depends on what are you going to count. For example, if you want to count positive immune cells better count number of these cells per 1mm2 or percent of positive cells to all cells in the power field. If you measure, for example, expression of some protein by cells, better use some scoring system.
There is no such best method standardised yet for IHC however depending upon the type of IHC it is best to compare with a positive control in the same slide adjacent to test section & should follow a standard scoring system where it is described for that particular marker.