Unfortunately I don't know of any good "Di2 for Dummies" type resource. You mostly have to use Google and read all the available user manuals, articles, forum posts, etc. and kind of piece it all together. I don't know if Shimano even publishes a generic Di2 User's Manual. They have individual manuals for each component (front derailleur, etc.) but I haven't seen much from them that ties it all together. Documentation isn't their strong suit anyway.
You can try starting with the Shimano dealer's manual, which I think covers almost everything, but I think it's pretty dense and hard to extract the information you need, especially if you don't know ahead of time what you're looking for. Here it is for reference though. This is for the most recent Ultegra Di2 but Dura-Ace should be the same.
https://si.shimano.com/pdfs/dm/DM-R8050-02-ENG.pdf
This is more readable but a bit dated in places (unless you have an older generation system, which you probably don't if the bike is brand new)
Shimano Ultegra and Dura-Ace Di2 Electronic Shifting ? Everything You Need to Know ? Carlton Bale .com
That button on the bar end junction box switches between several operating modes. If you just press and release quickly, I don't think it's supposed to do anything. But if you hold it in for a short time, you go into Bluetooth pairing mode (if you have a Bluetooth adapter installed). If you keep holding it even longer, you get a solid (red?) light I think, which puts you in adjustment mode where you can fine tune your front and rear derailleur trim.
If you double-click the button, you switch between shift modes, and the two lights will blink afterwards to confirm which mode you're in: 1 blink -> Manual, 2 blinks -> Shift Mode 1 (defaults to semi-synchro, I think), 3 blinks -> Shift Mode 2 (full synchro shift). If you don't know what the synchro shift modes are, then just make sure it's in Manual mode and the bike should work just like a regular mechanical groupset.
If you hold in any of the shift paddles for a second or so, the lights will give you a battery check (solid green means the battery is at least 75% charged). Then the lights will start to blink to confirm which shift mode you're in. So for example if you get a solid green, then the light goes out for a moment then both lights blink once, it means you're in Manual mode.
Finally, I have no idea why your e Tube software can't see the USB cable. Does the charging light on the cable come on when you plug the cable into the bike and your computer? If not, you may either have a faulty cable or something's not plugged in correctly.