How do you send signals through geological formations
For digital communications, bit error rate performance is all about $\frac{E_b}{N_0}$, the energy per bit divided by the noise power spectral density. The part that you can control is the energy per bit. Energy per bit is equal to $\text{(average power)(bit duration)}$. You can increase $E_b$ (and therefore decrease your bit error rate) in two ways:


Raising your transmitter power. This may or may not be possible based on the hardware you're using, the frequency band in use, and any governmental regulations for your locale.
Decreasing the bit rate (i.e. give more time per bit). In cases of extremely high path loss, like communication into caves, you can get reliable operation at a very low bit rate (although other issues such as long-term oscillator stability can come into play and diminish the gain that you might expect).


Communication into deep geological formations is something of a niche application, so you may have trouble finding a lot of literature on suggested approaches. There are companies who specialize in making this type of equipment, so it may serve you better to consult the marketplace for existing solutions that might be off the shelf instead of trying to engineer one from scratch (if your budget permits, of course; I expect such systems to be expensive due to the rather small market).