On the pro-audio equipment I used to service (ie Lexicon digital reverbs, etc, which were pretty cutting edge at the time) I recall that the supplies were completely seperate (as you have done), but joined at one place - the ADC converter.

If you join the supplies at the supply (would be more normal in a system where you are not doing ADC/DAC conversion) you have the problem that the the digital and analogue grounds WILL have different potentials at the all important converter, due to current flow back along the ground lines. That is the one place in your circuit where you cannot avoid digital and analogue circuits being physically close, and the internal operation of the converter may be affected by any offset.

Read the converter data sheet and app notes carefully. There should be some guidance.

You must obviously partition your PCB layout into seperate digital and analogue areas.

Just how far you go with this depends on what S/N ratio you need to achieve. In the gear I mentioned, the target was 16 bit performance with 16 bits = about 7V rms - means you are hoping to keep noise below 100uV, 20Hz - 20kHz - so they also took a lot of other measures - synchronising PSU switching frequencies to sample rate, and so on. The digitised signal was also passed back to the main circuit serially via optos, so I think that there was a 'quiet' (for acquisition) and 'noisy' (for computation) digital area as well.

For your purposes it's probably best to have seperate areas, and get as much physical distance between the uP and the busses and the analogue section as possible. Make the connection at the ADC, but with a 0 ohm link - when you test, you can try a link, a ferrite, a 100 ohm resistor ... see what gives the best results (there may not be much difference).