Thanks for your wonderful comments! I try to explain things simply because otherwise they're too hard for me to understand either!
Let me give you as an example, my own processing and clocking route as a kind of "template" that might help you. There are many variations on this, of course.
Assuming we're starting with a 44.1 kHz EDL in SADiE:
SADiE is on External Sync (you'll see where this is coming from in a moment)
SADiE's output 3/4 feeds an independent "jitter immune" DAC
This DAC feeds external analog processors
Analog processors return via Cranesong HEDD A/D on Internal Sync (Cranesong performs best on internal sync) running at 96 kHz. This effectively upsamples the rest of the chain to 96K and also allows the HEDD's digital processing to run at 96K, which reduces alias distortion (basically the HEDD sounds better this way).
Digital output of Cranesong feeds a chain of digital Processors
End of line of Digital processors at 96K is downsampled back to 44.1K in the Weiss SRC
This 44.1K signal returns into SADiE, which is effectively slaved to the downsampled clock from the HEDD, which also functions as the master clock for SADiE in this situation. And I can can cut a CDR master or reference LIVE this way. One hour after hitting play, the client gets a master! If I'm running my automation. But if the analog processors need to be adjusted on each song, or for some reason some function cannot be automated, then it becomes a song-by-song capture first, followed by cutting to a CDR master.
There are many variations on this scheme, depending on the sample rate in the EDL. If the EDL is NOT at 44.1K, then I capture the 44.1K output in Wavelab, acting like an independent "tape recorder", and I also make a simultaneous 24 bit, higher sample rate capture in SADiE for future DVD release, etc.
Of course I do not use analog processing all the time, nor do I use digital processing all the time.