What you said
One way might be a stamp based on what you want to use it for - answering questions correctly, excellent work or whatever you fancy. That would give you an idea of how many you could end up giving in a lesson. Then make the rule something like five stamps equals a merit. This way even the kids who don't get a merit still get a stamp. Unless you've been told you must follow the school's system, you could use your own.
When I was teaching, I would award, very sparingly, a public high five for outstanding work. There and then, while walking around the room looking at work.
The expert view
You seem to lack confidence in your own judgement. Although it is perfectly normal to be uncertain, children can sense it quite easily. One of the problems with the smileyfrowny face strategy on the board is that it takes up a lot of time. Partially ditch it. Keep a note of pupils' names in your planner and do it when you are ready and have time.
Make sure you have class rules that are clear and easy. Give merits for the best pupils in that lesson, for whatever reason you like. There is nothing wrong with varying the emphasis in each lesson as long as you let them know. And it is fine to give out merits for the three hardest workers, or best behaved, or kindest, most improved, and so on. Your classroom. Your call.
Tom Bennett's latest book, Teacher, is out now, published by Continuum Post your questions at www.tes.co.ukbehaviour.