If your processor is fast enough and you have the skills, you may let the processor generate the output frequencies using PWM or a DA converter. And you may use a AD to sample the received data and run two digital filters to detect the two frequencies.

Another way is to build a two-frequency tone generator and have the uC enable one or the other frequency for transmission, and to build a frequency detector and have the uC check if it detects any frequency.

An easy way to implemnt the FSK functions outside the processor is to make use of a modem chip. For example a CMX869B has a number of preconfigured transmit or receive frequencies but also support for user-configurable frequencies. It communicates with the uC using SPI.

Software-based decoding is easier if you don't need so high baudrates, since you will then have longer tones - more periods - to analyze. With enough periods, it is even possible to just analyze the zero-crossings of the received signal - but that puts some extra limitations on the signal-to-noise ratio of the input signal.