Where do i start?
You begin the game with your home planet, a shipyard, and a few construction ships. If you click on your planet, pretty much everything can be controlled from there. There's a button for planetary upgrades (they're all pretty self explanatory), another for building logistics buildings (resource harvesting mines, shipyards, research labs, trade ports, etc), one for military buildings (defenses and such). On the bottom row you will have buttons for any shipyards you have in the gravity well of the planet, so you don't need to select individual shipyards to build any ships. There's also a set waypoint button that the ships you're building will obey.
To start, select your planet, click on the logistics buildings button (looks like a gear), and you will see most buttons greyed out. On the very left you will see active button to build metal and crystal mines. As a general rule, most things you colonize will have resource asteroids around them that you build mines on to gather ore and crystal (these never run out, and are completely automated). The planets themselves give you credits through taxing the population, so the higher the population the more money the planet makes for you.
Next, with the planet selected go back to the root menu, and click the "Frigates" button on the lower bar. You will be able to build scouts, colony ships, and basic attack frigates at first. For starters, build a scout. Select it once it finishes and you will see it has an "explore" ability. That means it can fly around the map discovering all the planets and nifty things. For now, just right click anywhere in the planet's gravity well to get the ship moving. Now, zoom out until you see a white line (or more) leading to a greyed out planet with a (?) over it. That means you know there's a planetoid there, but you haven't discovered it. Right click on that planet with your scout selected, and you will tell it to phase jump and map that planet for you.
There's 2 kinds of movement in Sins: One is moving normally around each planet's gravity well, and the other is phase lanes linking planets (and stars). Giving your ships an order to move to another planet will make them fly to the edge of the gravity well of their current planet, and then phase jump to wherever you ordered them to.
Now that you know how to move ships around and build buildings and such, start experimenting! Sins is just one big giant sandbox
It's very hard to describe everything you need to know, so if you have any specific questions please post them and I'll answer them
In the meantime, I hope this is enough to get you started.
