As others have said. Break it up into managable pieces.
For me I'll usually step through the following process. Mostly by going through a combination of the in game tutorials, youtube, Chucks guides. Well before I hit the manual for fine tuning. Additionally in regards to Chucks guides, they are brilliant for jumping straight in and as a reference later on. ED and the third party developers should be paying him so they can ship his guides with their modules.
On first session I'll usually hit up:
1. Initial controls setup (I usually try and get a 1:1 match with the real aircrafts HOTAS setup) Figure out quirks for basic universal features such as flaps, taxiing and airbreaks.
2. Aircraft startup procedures - I usually make a habit of trying to do cold and dark starts as much as possible.
3. Radios
4. Navigation Equipment inc. Autopilot
5. Testing skills learned by throwing a mission together to test startups, navigation, comms, refueling, takeoffs and landings.
The above tend to be universal, it's just learning where the knobs and switches are placed and any idiosyncracies. Get some of these out of the way before moving onto the more fun stuff.
6. More critical misc systems such as Countermeasures and Radar
7. By this point I'll start iterating through weapons systems. I'll try one type of system with one type of delivery method at a time, usually the ones most relevent to my interests first. Get the basics out the way.
8. Once I'm comfortable with general use I'll start probing into more advanced systems such as the additional MFD content, advanced weapon delivery, waypoint management etc...
But... that's the method that works for me. If you want to get started slinging weapons at targets you can skip a few of the above. Step 1. is always critical but you can always find a quick youtube video for getting your nose pointed in the right direction and how to get stuff off the rails. Break it down, figure out what's relevent to you. You want to do online? Spend a little time on your radios for SRS. SRS Should also be shipped with DCS as a default.