"Make it count" is a way of saying "do (something) in as positive and useful way as possible." Don't just throw an opportunity away by only putting half your heart or effort into it -- make it really matter, try your best, do your best. Maybe the most common example is: "You only have one life to live, so make it count." Don't waste your life by only doing what you need to do. Go enjoy life fully, have adventures, give friendship and love to other people, make a difference by doing work that improves the world, etc.