Sir, First you should be aware of the information on haemocytometer that you are using to count fungal spores. Its depth as well as volume. Than the rest is easy. You have to count spores randomly from the five big squares, Generally there are nine big squares, each square is subdivided into sixteen small squares, if the fungal spores are big than count them in big squares, if small spores then focus on small squares. each square has a certian area.
You can apply the method outlined in the attached file, could be useful. Also, there are very good video in Youtube explaining the spore counting by Hemocttometer