The ground connection for the bottom capacitor besides the crystal looks wrong, because the blue trace is below the SMD pad, which won't work without a via, and you can't put a via inside a SMD pad. Note also that the ground path of the two capacitors beside the crystal should be a very short connection to a ground pin on the microcontroller, because at higher frequencies any detour acts as stray inductance etc.

The usual way is to use the bottom side mostly for ground, then place a via between the two capacitors to the ground layer and another via near a ground pin of the microcontroller, and careful routing it in a way that at the ground layer there is no trace between it that causes a longer path. Usually I route any bottom and top layers with wires, so that I see how the current flows, and do the polygon fill at the end.

Another important thing, because I can't see it in your layout: you should add a 100 nF decoupling capacitor near your Atmega, and another one near your RTC. They should be connected between a VCC and ground pin, again with shortest path.

Is it not possible to place vias under a smd part, because under the Atmega is pace.. I will post a further image of that.

Yes the caps are placed, and i will rotate the crystal again to the nearest point.

Yes, you can place vias under the Atmega.

i think its better that iam placing the planes at the end ? So the other traces are better to see.. or is there a dedicated layer for this ?

you can hide the polygons by ripping them up, otherwise it would be indeed a pain ;) but it also helps concentrate on non ground stuff - less airwires and all.

That looks so much better already :) you still checkout ground planes :)