I can’t offer advice on the best engraving software, but I can suggest getting to know at least Carbide Create. A full CAD package (like Fusion360) is real nice if you are doing more than basic engraving.
For fixturing, the threaded palette with cam and jam clamps is great for a lot of things, but the MDF wasteboard serves many purposes as well or better. Don’t be afraid to screw into it. You can make or buy more (I’d suggest adding the 5-pack of spare wasteboards to your order). Don’t be afraid to glue to it, cut into it, drill it for fixturing pins, or any other thing. That is what it is for. Do keep in mind that it may not be dead flat… there is a tolerance. But it will be close enough for many things.
For repetative work, drilling a few holes in the wasteboard for locating pins and/or holding screws can make your life much easier. The Carbide software has a few hardware referenced points that it can reference easily, and they are very nice for setting fixed points for fixturing.
I have a threaded table that gets a lot of use (not the C3D one, as it was not yet available at the time I purchased), and it is key for certain precision work. If you are not doing machining of parts to 0.02mm, you will do fine without it.
Without more information about what you are trying to engrave, and what other jobs you might use the machine for, it is tough to get into real detail.
As for taping down your work: it is quite effective, but requires a little care. I use a Nitto tape for a lot of things, and 3M 467 for things that need precise level (it is a linerless adhesive with very well controlled thickness of about 0.05mm, holds like a champ, but can be removed more readily than, say, canoacrylate). I also use these on the lathes, metal shaper, and full size milling machines. Good adhesives will surprise you.
I’ll shut up now…