Scott,
This will cause debates
Obviously, there is going to be a learning curve with any DCC system if you have never used it before. My way of thinking though is to buy your first system that makes that learning curve easiest and with less frustration.
My first DCC system was the Digitrax Super Chief, similar to what you bought, and it was easy to setup - basically plug and play; however, that is where the "easy" stopped. The instructions that came with it were full of "presumed prior knowledge" (like all Digitrax stuff) making them difficult to understand and follow. As such, pretty much everything beyond the initial setup was a pain in the rectum.
I persevered with the system for almost 12 months before I (literally) threw the thing out into the yard and bought myself an NCE Power Cab Starter System. The initial setup for the NCE was just as quick and easy, plug and play; however, the programming of engines was far easier AND clearer with very little "presumed prior knowledge" incorporated in their step by step instructions.
In short, there is going to be a learning curve with any DCC system that you first get; but the difference in that learning curve between Digitrax and NCE, in my opinion, is like night and day.
I should qualify my statements with this, I am not the most technically minded person on the planet so that didn't help with the Digitrax learning curve, which was more like a lot of hairpin bends rather than a curve. If you are technically minded, the Digitrax curve may not be as bad for you.
When all is said and done, Digitrax is good stuff but is more complex to use. NCE is also good stuff but, for someone who has never delved into DCC before, is easier to come to terms with.
In so far as the engine you bought, your right, that doesn't matter so long as it is has a DCC decoder installed. What you need to know about decoders is MOST come from the factory with a default setting 03 for your engine. The 03 is the "code" given to the decoder for the engine and what your controller will read. Every time you buy a new DCC engine, the decoder will set to 03. Therefore, if you have 3 engines on your layout straight out of the box your controller will read all of them as one engine so when you run 1 engine, ALL of them will run. In order to run each engine individually, you need to program (using your controller) in a new "code" for that engine (normally the cab number) and that is where things can be easy or a little complex and that is where the difference between the Digitrax and NCE systems come into play.
Your initial question, will it take you all day to run one engine with your DCC system - NO it wont. Will it take all day to run 2 or more engines individually - it could.