I'm gonna take a shot at this because I *think* I understand what scmbag's trying to describe.... I had the same prob, being self-taught on Flexi. Stewart's got the idea there.
You're describing cutting letters that have an outline. Sounds like you're trying to determine how to cut the letters themselves, and then the outlines themselves, and you want to make sure that the letterforms and their outlines line up perfectly so that there is no sliver of background showing through?
The answer is simple and saves you LOTS of work. It did for me.
When you create an outline, the Design Central floating palette shows a tiny button, either red with a black outline ("with backing"), or black with red outline ("without backing"). The state of this button determine whether the outline is a true outline, only existing around the outer edge of the letterforms, or whether it is an entire solid background behind the letterforms.
If you create outlines With Backing selected, then it is an easy task of cutting the background vinyl (the outline), then cutting the foreground vinyl (the letters), and laying them down in a 2-layer stack onto the substrate.
If you add a shape, such as a small triangle, at each end of the lettering, and cut it out with both layers, then you can use them as "line up marks" when laying the top layer down on the bottom layer. This way there is no question about making it line up perfectly centered. Afterward, peel them off and you're done.
Hope this answered your question.