I’m not sure about this, but I would be concerned that going through the S1 first to the L1C wouldn’t get an optimal signal to the L1C’s subwoofer. I would lean towards going into the L1C first then daisy chain to the S1.
Do what works and sounds the best for you. Here are some ideas.
Source(s) to S1 Pro to L1 Compact
As you know, the S1 Pro is more flexible than the L1 Compact with respect to the inputs. (Two combo input channels with ToneMatch Presets, Bass, Treble, Reverb).
If you are using two channels and you want reverb in both the S1 Pro and the L1 Compact, start with the S1 Pro and connect Line Out to the L1 Compact.
Note: The S1 Pro line out is "post-fader" and that means anything you do with the S1 Pro channel controls flows through to the Line Out. If you increase the bass, then the Line Out will have more bass. However, the processing for Auto EQ and protecting the S1 Pro woofer does not affect the Line Out.
Source(s) to L1 Compact to S1 Pro
If you like the sound when you connect your source(s) to the L1 Compact, then put that first in your signal chain. Here are some reasons why you might prefer that signal to L1 Compact line out to S1 Pro.
You are using the L1 Compact as a Front of House system (sound going out to the audience) and
You don't want (excessive) reverb going to the audience
You are using the S1 Pro as a monitor and you want different tone and reverb effects in the monitor sound than you are sending to the Front of House