You are asking a lot of questions that go in a few directions so I will try to answer and be clear. The learning center classroom has great tutorials on all things and I recommend watching those again if you have not already done so.
If you are going to "write" words on a material, you either need to use the pen tool with a permanent marker (which works beautifully by the way) or engrave it into the plastic. The engraving tool has a sharp diamond head, but using it on plastic will wear it down over time. You might want to rethink the engraving part - or try it with pen/marker first to see how you like it. And remember that not all fonts engrave the same. You will need to fill some with a cross hatch pattern or use single line fonts. If you use the pen tool you could at least play with that to get the font that you want and then try engraving it. The pen will also give you a faster result - engraving takes time depending on the hatch fill etc. Lots to consider.
You can certainly use the cutting blade at a lower pressure to score a material by creating dashes or even long lines at a lighter pressure to fold. But it's a blade so it isnt going to give you letter detail - you need a pen or etching tool that has a center point and tip to do lettering of any kind. You could also use a labeler and create a tape label for the stencil - again options for you to consider so you can try different things and see what you like best.
The information you are asking about is in the learning center. But if you have a shape like a stencil, that will be one layer if you group it. You may not need to group it - depends on the image. Then if you add lettering that will be a different layer automatically. So you would close the eye of the stencil, just do the lettering however you choose to do it with WYSIWYG, turn off the eye of the lettering and turn on the eye of the stencil, change the blade and pressure and cut the stencil. Make sense? That's the short version.