SWG and VS pump share a time clock

Welcome to the forum.
The VS pump wiring should come from the Line Side of the timer. Typically 1 and 3.
The SWCG wiring should stay on the Load Side so it can be controlled by the timer.

Post pictures to ensure this is how yours is set up.
 
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No need - it's already wired to the line (hot) side of the timer.

Does the conduit exiting the left side of the time box run to your SWG?
If so, the SWG is wired to the load (switched) side of the timer.

Does the pump run 24/7 or does it switch on/off daily?
If the pump doesn't run 24/7, you need to add the ON/OFF timer cogs onto the timer wheel to cycle the SWG off during times the pump is off. The SWG flow switch is a secondary safety device - the timer is the primary safety device that turns the SWG on/off. Many of us have the timer to power the SWG on 30 minutes after the pump starts and power the SWG off 30 before the pump shuts off.
 
No need - it's already wired to the line (hot) side of the timer.

Does the conduit exiting the left side of the time box run to your SWG?
If so, the SWG is wired to the load (switched) side of the timer.

Does the pump run 24/7 or does it switch on/off daily?
If the pump doesn't run 24/7, you need to add the ON/OFF timer cogs onto the timer wheel to cycle the SWG off during times the pump is off. The SWG flow switch is a secondary safety device - the timer is the primary safety device that turns the SWG on/off. Many of us have the timer to power the SWG on 30 minutes after the pump starts and power the SWG off 30 before the pump shuts off.
Yes the conduit on the left side is going to the SWG. I had a company open the pool they set the pump to run for 10 hours on the internal timer, I later set it up for a 24/7 schedule. The thing is I went out to check it one morning and the pump was off , I’m assuming because it is set up on the the external time clock ?