Suggested approach-
If I'm recording the digital input, and often even if I'm not, I just leave the machine set to record a digital input to the stereo channel. That's partly because I find doing so more straight forward and user-error-proof than recording a digital input to channels 5&6. To record digital input to 5&6, in addition to setting 5&6 to DIGITAL on the I/O menu, you must also remember to set all channels to record as stereo files on the record menu. It won't work if set to record individual mono files. If the digital-in is sent to the stereo channel instead, it doesn't matter if mono or stereo files are written for the 6 main channels (the stereo file is always a 2 channel interleaved file).
And, because I usually don't care about recording a live stereo mix, I can just leave ST REC set to DIN. That way, regardless of my file output preference, I don't need to go in and change any menu settings when I'm doing any of the following-
1) recording analog inputs only, using the recorder's internal clock.
2) recording analog inputs only, syn'cd to the digital input clock.
3) recording both analog inputs and the digital input, syn'cd to the digital input clock.
I only need to arm whichever inputs channels I want to record, regardless of the combination of digital and analog inputs I happen to be using.
If no digital input is attached, the recorder will report DIN UNLOCK upon entering record or record/pause mode, but will record normally using it's internal clock. That message can be dismissed by pressing the enter button or with a push of the control knob and the recording proceeds normally using the internal clock regardless of the message being displayed or dismissed.
The only time I'd consider recording the digital input to channels 5&6 is if I either wanted to record a live mix of the first 4 analog inputs and the digital input to the stereo channel (I think that's possible, never tried though), or if I wanted to be able to simultaneously playback the recorded digital input channels and the first 4 analog input channels the from the machine.