There are several possibilities to pause a slide. The easiest one is to use an interactive object: button, shape button, click box or Text Entry Box. They all can have a pausing point (visible in the Timing Properties panel). The timeline is the core of Captivate, where you can time objects to appear later than the start of the slide. Your question is very basic and very vague at the same time. You are talking about 'an effect'... are you pointing at the Effects that can be applied to an object? Those effects have their proper timeline.
Try to avoid the simple action 'Pause' at the Exit event of a slide, it will stop the movie at the first frame of the next slide which is not what you want. Only for very specific situations do you need to pause with an advanced/shared action. I don't know why you think it has to be done so often?
This is an old blog post about the timeline, although the screenshots will not be totally the same, most is still valid: Tiny Timeline Tidbits - Captivate blog
You talk about master slides: if you want to create a custom navigation with buttons, you have to know that only shape buttons can be used on master slides. If the shape button is set to pause, it will always pause at the end of each slide, whatever its duration. Because on master slides you cannot time anything. Why I like Shape Buttons - Captivate 6! - Captivate blog explains some use cases for shape buttons.