I agree with Pepper- too many different ideas to count. The best idea IMO is the one I found in The Herpetoculture of Leopard Geckos. You just use a piece of tile as the floor and a couple pieces of PVC pipe as legs. Have the legs only about 2" tall so that the gecko can easily climb up to the level. Plus, the tight space underneath would act as a big hide/cave. This way your second level is removable, easily cleaned, and as long as you secure the legs properly, very safe.
I've compiled a list of links of pictures and tutorials on how to build a second level, fake rocks and fake rock walls. This was helpful for me, so I thought I would post it for other people: