The reference to Counting or Not Counting within the MyEG app is talking about rounds that are or are not included as part of your Handicap Index®.
To start building up a handicap index you need to complete 54 holes, through either a combination of 18 or 9 hole rounds. At that point your H.I.™ will be based on the best Score Differential™ of those three.
From that point your HI will become more reflective of your playing ability up to the point of completing 20 rounds, at which point it will be an average of your best 8 Score Differentials (plus taking your low index into consideration).
Following is a table that explains how your HI is calculated until you have completed 20 scores.