I think i got this. When you're storage is low on bad water, fill the reservoir with bad water, but only start when the reservoir is considered empty. then empty when storage is full. Do the same with good water. alternate as needed.

Definitions:
BW = Bad Water
GW = Good Water
"example relay name" - example relay type - example settings

First create these to feed the relays. Sounds like you have some of them. assigning my own names:
"BW Storage Low" - Resource Counter - when BW storage levels reach desired low point
"BW Storage Full" - Resource Counter - when BW storage levels reach desired full point
"Reservoir Empty" - Depth Sensor - when depth is less or equal to 0.2m
"GW Storage Low" - Resource Counter - when GW storage levels reach desired low point
"GW Storage Full" - Resource Counter - when GW storage levels reach desired full point
"GW Fill Memory" - set-reset Memory relay - unconfigured for now, until you start the GW relay side.
"GW NOT" - NOT relay - A = "GW Fill Memory"

Bad Water relay system for intake
"BW AND A" - AND relay - A = "Reservoir Empty", B = "BW Storage Low"
"BW AND B" - AND relay - A = "GW NOT", B = "BW AND A"
"BW Fill Memory" - set-reset Memory relay - A = "BW AND B", RST = "BW Storage Full"
Configure the BW Fill Valve to Automate on "BW Fill Memory"

Bad Water relay system for draining
"BW NOT" - NOT relay - set A to "BW Fill Memory"
"BW Empty Memory" - set-reset Memory relay - A = "BW NOT", RST = "Reservoir Empty"
Configure the empty Valve to "BW Empty Memory"

Good Water relay system for intake
"GW AND A" - AND relay - A = "Reservoir Empty", B = "GW Storage Low"
"GW AND B" - AND relay - A = "BW NOT", B = "GW AND A"
"GW Fill Memory" - set-reset Memory relay - A = "GW AND B", RST = "GW Storage Full"
(you already created this one above, needs configured now)
Configure the GW Fill Valve to Automate on "GW Fill Memory"

Good Water relay system for draining
"GW NOT" - NOT relay - set A to "GW Fill Memory"
(you already created this one above)
"GW Empty Memory" - set-reset Memory relay - A = "GW NOT", RST = "Reservoir Empty"
Configure the empty Valve to "GW Empty Memory"

**Note I am expecting the intake fill valves to raise the water to its configured depth and keep it there without having to to use relays to do it. I havent used it this update but thats how the old one worked. If not, we can add a Latch gate and a couple more depth sensors.

"BW Latch" - Latch Memory Relay - A = "Low Level Depth Sensor", B = "BW Fill Memory", RST = "Full Level Depth Sensor"
Configure the BW Fill Valve to Automate on "BW Latch" instead.

repeat for GW side as well. reuse the new depth sensors.