When I installed mine (years ago) I believe that the instructions showed that approximately 3/4" of preload was recommended on the springs. With the spacers that came with my kit, they needed no trimming to achieve this, but it is possible that the spacers (really just PVC pipe I believe) that they now supply may be different length. You'll want to have to compress the spring/spacer combination this much to get it into the tube and under the top plug/circlip. If you don't have enough preload, the springs will rattle in the tubes when the suspension tops out and the overall suspension action will be odd.
I think that I put my springs in with the close wound part of the spring toward the bottom, but can't be 100% certain.
You could put the spacer at the top, though this could make pushing the spring & spacer downward into the tube to re-install the top circlip and plug a bit trickier, and it might be noisier that way too (I don't know). But, at least it would be a little easier to remove them later if you expect you might have to.