Have you found the Wiki? There isn't much of a beginner's guide there, but it did help me understand most of the mechanics of the game. Stuff like influence I don't know how they expected a player to just pick that up. Being turnbased you have the luxury of not having to work under time constraints (not multi-player obviously) so I recommend putting your alt and tab keys to work and consult the wiki as much as you need to in game.
With games that have so much to learn like this and Dwarf Fortress, my method for learning is to start a game with a single goal in mind. For example you could start a game with the sole intention of exploring the diplomacy mechanic, and see how well you can do with just trade routes and trading research and resources with your allies. Once you get a good idea of how that works, abandon that game and start over but try and focus on keeping your planets satisfaction up. Another time try and maintain a HUGE army and teach yourself organizational tricks to keep track of all your fleets. Eventually you can piece it all together and dominate the galaxy.
There is no single resource that will allow you to just "get it" the game is too in depth for that. Just play, learn and have fun, it's a great game.