I recommended editing a camera as an easy way to extract the *.sss file from a zipped archive — get SE to actually do it for you by writing a new file.
But if you're familiar with extracting files from zipped archives, that is always best, I suppose.
If you have the Merlin, by all means, give it a try. It is a very well done model. (No warp drive, though, I do believe.) Your idea of a great cockpit view may be different from mine.
Main engines are just that — the main engines, that gives you thrust. Used in orbit, used in atmosphere. But hover engines can be useful in atmosphere, too.
I've done very little ship editing in 990, mostly in 980. And I don't know if Vlad has updated his "Build A Ship" tutorial on this website, so I have no idea about the "Aeromodel" parameter. Actually unaware of it until you mentioned it. I have no idea what other, if any, options are available.