So I have a 1999 Baja 252 Boss, it has 2 batteries, with a switch.

after 3 years of never leaving them on I messed up and left the boat setting in the yard on battery number 2. well when I put the boat in the water, I cranked it on battery #1, and then swapped back to battery #2 (to charge it back up)

but when I went to lower the drive all the way down, this killed the motor. I tried a few ways, with and without the motor running.

battery switch on #1, trim does not work. (everything else does cause #1 is a good battery)

battery switch on #2, trim does not work

but when I put it on BOTH. everything works. so the conclusion I came up with the power trim is only connected to battery #2. because it does not work by its self, and does not work on one, but on both its sharing power from the good battery, and still has #2 connected.

is this correct? seems like the trim should work on either battery.

Sounds like trim pump pos. wire is hooked to batt #2. If it is remove it and put it to common lug on batt switch and it will work on either batt.

yea thats what i was thinking, but is this normal? or did someone move things before?

When it comes to boats nothing is normal. Could have come from factory or been changed along the way. Sometimes people want to be able to use trim without turning on switches when trailering boat.