How can I connect polygons 1 and 2 together? It tried to make a trace + vias between them, but Eagle won't let me create a trace on a polygon.
You should be able to create vias in the polygons, name them to match the names of the polygons, and then connect with a trace. If a conductor (via or trace) does not have the same name as the fill (polygon here), then Eagle will add space to prevent the signals from shorting together, as happened with the CSN via towards the side of your picture.
You could do this with just appropriately named traces too, but I don't see how you can do it without vias in this image.
As this answer implies, both polygons need to have the same name to be connected.
To do this without adding the via, you can add an arbitrary trace by going into Route mode and ctl-clicking inside the polygon. That method can be a bit wonky, so it might be easier to add the vias, make the trace, then remove the vias.
- Give the two polygons the same name. That way Eagle knows they are the same net, and will allow you to directly route other traces of the same net to them. This includes a trace between the two polygons.
- Give them different names, then connect those two nets with some kind of part in the schematic. I have a library of "shorts" for this purpose. They are parts that just end up being a connection in the schematic, but allow the nets on either side to be distinct. This can be useful, for example, for funneling all the power current for some section thru a particular point you can choose during layout.
You can connect these two polygone by adding a via and a trace on the TOP layer. To do so, add a via on each polygon and name them "GND" or the name of the polygone surface.
It is maybe possible to redesign a part of the PCB in order to avoid this durty solution.
Another way to solve your problem could be to make a route across the resistor between the pad. To achieve this you may need to edit the PCB properties, or resistor pad's shape.