Like this:
First tune the Low E, then the high E, then the A, then the b, then the d, then the g.
Now, when you come back to the Low E and it's still out of tune, you must compensate. Lets say your tuner says that the Low E is 2 semitones flat (or 2 dots on your tuner). Tune it 2 semitones sharp. And repeat with the rest of the strings.
That should solve your problem.
If not, you need to make sure that the bridge is in the right position. Which is pretty much parallel to the body of the guitar. If not, you need to adjust the springs in the back of the cavity.
Hope that helps.
Sometimes I hit notes only dogs can hear.