Looking at my 98 manual, it's not real clear if there are two timers or not. In earlier models, the same timer was utilized for both Aerate (Fill) and Hydro (Recirculate). Auto position for each switch runs through the timer and the Manual position bypasses the timer and runs the pump continuously. If there are two timers, it would appear that the Aerate timer is fixed and probably a module behind the switch panel. I would need to get behind the switch panel to see for sure.
bukfevr, does the knob on your Hydro switch also control the time for the Aerate in Auto mode?
So, there are two ways to manage your livewell. One is to fill the livewell with the Aerate to the desired level. Then switch on the Hydro to recirculate the water. This is the most common especially during hot months when you may have livewell treatment and ice in there to control the water temp. Here in TX in the summer months it's common for surface temps to be in the mid to upper 90s, so it's standard practice for me to cool down and treat the water in my livewell. The other method is to use the Aerate to fill the livewell then switch the Aerate switch to Auto. This will, like Lea said, draw in fresh lake water when the timer turns the pump on and excess will exit via the overflow. I use this up until about May when I switch over to the closed method, then will use it again in the fall after the surface water has cooled to 70° or less.
Leasure Lectronics makes a couple of different variable timers that could be used to replace the one you're missing.
https://www.ebay.com/i/173632441147?...SABEgKAPfD_BwE
One thing I did note was an option for pumpout shown in one of the livewell plumbing diagrams, but no switch on any of the schematics. All the Bilge switches were just on/off switches. So, I'm thinking that was added to yours by a previous owner.
Good Luck with your project! Holler if I can be of any asistance. I've got ~50yrs in electronics, DC & RF and pretty familiar with the systems in our Champs.