Eh, kinda common sense really.
Example: I want to build a basic station consisting of 3 main modules: a core module, hab module, and a science module.
Okay. common sense dictates that I send up the core first, but the core needs to be powered, it can't fly up alone. So, it needs a module to provide solar power (for this example, the core contains all life support systems.) But a solar array can't hang out in space while I ready my next flight. Okay, so we'll use Zarya, since it's designed to be a utility module.
Flight 1: Zarya to orbit.
Alright, our preliminary power source is ready, time to send up our core and dock it. We'll also send up a PMA, so our ship can dock with it too.
Flight 2: Core rendevous with Zarya.
Awesome, our core is powered and providing stable life support. We can't facilitate a crew however, unless we send up Zvezda or a hab module. In this case Zvezda can accommodate two members and provide us some extra life support, and it even power itself, so lets send that.
Flight 3: Zvezda to station.
Okay, we're ready to get a small crew up there, let's do that.
Flight 4: Crew to station.
Now, let's see about attaching that hab module, since we'll need much more crew than our current crew to sustain the science module.
Flight 5: Hab module to orbit.
Alright, we're ready to attach the science module, but the power draw will exceed the capabilities of Zarya and Zvezda, so let's get some panels up there.
Flight 6: Solar Array to orbit.
Okay! We're ready for our science lab! Send it up.
Flight 7: Science module to orbit.
Now, all that's left is to send the research crew.
Flight 8: Research crew to orbit.
If you want, you can even send up resupply missions, should you wish to actively keep the station. As for placement, just try it out in the sim. Spawn the modules in and fiddle with the placement of your RMS systems, docks, module placements (after all, having half your station shear off when your XR5 opens its payload bay is a problem, and it's a massive waste if your RMS can't reach the spot where you want to place your module.)
That's really all there is to it, everything else, how to get up there, the modules in question, are entirely up to you.
EDIT:
My Trinity Station is in very early assembly. But even so, I had early problems with RMS placement, because I went on the fly. I actually had to send a mission to relocate it on another module. From there, I actually planned out, like Cras, on a spreadsheet, so that way I won't have to worry about it, and it's going swimmingly now.
