I can't say that I buy the whole 'it sounds better with an external clock' thing either - I've tried the wordclock both ways 02R>828 and 828>02R and I couldn't hear any difference. I also tried it at the studio with the DM2000 and dual 828 units but again, it made no difference.
Configuration wise, I'd have it so the 02R is very much at the centre - my little home studio requires virtually no re-configuration whether I'm recording or mixing. Between the analog and ADAT I/O and using the S/Pdif as a return, it's a great solution.

My home config:
Out..
Control Room > Main monitors
Studio Output > Secondary monitors
Slot 1 ADAT Direct Out 1-8 > ADAT A in 828
2-Track S/Pdif Out > S/Pdif in 828
In..
Slot 1 ADAT in < 828 ADAT A Out
Slot 2 ADAT in < 828 ADAT B Out
Ch 9-16 in < 828 1-8 Analogue Out
Ch 7-8 in < 828 Main L-R Out
Ch 1-6 in < Instrument / Mic
TC Unity A external ADAT in < TC Unity B Out
Internal..
Aux 1 > TC Unity A FX Unit 1
Aux 2 > TC Unity A FX Unit 2
Aux 3 > Spare Out
Aux 4 > Spare Out
Aux 5 > TC Unity B FX Unit 1
Aux 6 > TC Unity B FX Unit 2
Aux 7 > Internal Yamaha SPX FX Unit 1
Aux 8 > Internal Yamaha SPX FX Unit 2
Stereo Ch 17-18 > Subgroup 1-2
Stereo Ch 19-20 > Subgroup 3-4
Stereo Ch 21-22 > Subgroup 5-6
Stereo Ch 23-24 > Subgroup 7-8