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I have just adjusted my spacers positions on my headset. There origionally 3 spacers below the stem one larger than the others and none above the stem, then I took the 2 smaller ones and placed them above the stem, will this affect the gap between the steerer tube and the top cap, (even if that matters). As I am unsure because I was thinking as long as I have the same amount of spacers on the steerer tube then it doesn't matter, or is there importance to do with the position of the stem?
You are fine and your understanding is correct. It's the total stack height of the spacers and the stem between the top of the headset and the cap that matters, so spacers can be swapped from below the stem to above and vice versa to adjust your stem height as you like it.
You can have all the spacers you want above the stem on a steel or aluminum steerer.
On carbon, some manufacturers use a wall thickness where their specified compression plug acts as a reinforcement for the clamped area. In most cases this will apply to the kind of plug where the part you turn down consists of thick aluminum that contacts the steerer ID all around. And because it's only so tall, that means you could be lacking sufficient reinforcement if there's too much spacer on top. I wish this wasn't true, but it is. In practice, one 5 or even 10mm spacer would likely never be a problem. But it's a good boundary to leave unpushed.
