there is no break in, just monitor their temperatures and keep a keen nose for any coil smell and slowly raise the gain while playing music for a few minutes and seeing how things sound and monitor the temperature. If it can play for 5 mins straight without heating up or smelling then you are fine.
How's the overall sound? You can start playing with the crossover points to see what works with what. Use the EQ to correct any harshness etc... make sure loudness is not turned on in the head unit.
For position, make it front left, then go to your speaker level and make sure they are all evened out(except sub, you can decide what you want on that) Then go to the time alignment and measure out the distance from each tweeter and mid to your ear and enter in the measurements.
Afterwards just play around with the numbers aka adding or subtracting both tweeter and midrange values (left or right doesnt matter) while playing music until you feel like the singer is dead center on your dash.