Electronic – problem to solder only one side of a dual PCB

To be honest, I don't see any problems, though I have read the question twice now.

I don't even see any problems soldering the RTC, as an SO8 package really isn't that small, even for a hand made PCB. What's your PCB production method?

To maintain good accuracy, you might consider keeping the circuit at a controlled temperature. You could use a Peltier element plus a thermistor to regulate the temperature.

There are such things as temperature compensated oscillators (TCXO) and Oven Controlled Oscillators (OCXO), but these don't seem to be available at 32.768kHz.

While I have to agree with the previous answers - you are indeed a lot better off in the long run if you route manually, I feel your question has not really been properly answered.

A quick-and-dirty workaround for you might be

• copy the component(s) to a library of your own
• add a new package, in which you put a GND rectangle around the entire component on the top layer only
• in the circuit, replace the original component with your tampered component
• let the autorouting commence
• go back to your circuit, and swap the component back to its original package.

Now, before the rotten-egg-throwing sets in, a few extra words why you should not do that.

While Eagle takes quite a bit of effort to get the hang of, it is definitely worth practicing these things on simple designs. As you advance, you will get to the point where you have to route manually, because some signals must be laid out in certain ways. There might still be workarounds for each specific problem, but you will never have practiced to place the components in a way that it is possible to route with minimal effort and losses.