There are many different ways to skin this cat. You may get lots of opinions.
Here's one.

Run the battery cables to what we will call the start battery. Alongside of the start battery will be what we will call the house battery.

The start battery only starts the motor. It does nothing else. The house battery normally only provides power to all of the other stuff in the boat. I say normally because in an emergency it can be used to start the motor.

Between the two batteries will be a combiner. I like the Yandina brand. Combiner 100 Sheet

Once the motor is started the engine generator will recharge the start battery. Shortly thereafter it will parallel the two batteries. Parallel is a fancy word for connecting the two batteries together in a certain manner.

Both batteries will be charged at any time the motor is running. Once the motor is turned off the combiner will disconnect the batteries from each other. You can fall asleep in the hot summer sun with the amplifier playing tunes and let the house battery go dead. Does not matter. Use the start battery to start the motor and in a short while it will start charging both batteries again. Let the motor run long enough and it will fully recharge the house battery.

Here is a diagram for the configuration that I used. It is almost fool proof, unless a better fool comes along. All switches are off when the boat is not being used. When using the boat turn on just two switches. One to the start battery and one from the house battery. Leave the transfer switch off. At the end of the day simply turn off the two switches.

If and when the start battery should ever go dead you would turn off the start battery switch and the house battery switch. You would close (turn on) the transfer switch which will then feed power to the motor from the house battery. Start the motor. Then close the start battery switch so that the engine can recharge it. Open (turn off) the transfer switch. Close the house battery switch to provide electrical power to the boat stuff.

Okay the reason why I ask is coming from the motor on mine there is a positive and negative big cables then it has a red small And a black small cable

Where do the small cables come from and where do they go? Where do they connect on the motor and to what device are they connected?

Can you take and post a photo of the smaller cable?

Oh, the F90 is not the same as the F150. The F150 has the capability of installing an isolator lead to a second battery whereas the F90 does not.

I will have to do it tomorrow when I get home thats why I was wondering if it was like the F 150 when I saw a small red one and a small black one

so the combiner go between the two positives of the batterys thank you for your help I'll check tomorrow and see where they go and post a picture

the F150 has a battery isolator built into the engine wiring harness.
no need for anything other than the lead and a 50 amp fuse.
post a model number of the F90 and I will try to remember to look and see if that F90 has the same isolator.

2011 f90 tlr

Sorry I have not had time to dig into the motor area to see where the small red and black cable go they red cable does have a big square like a fuse block or something

I haven't found any info yet.
can you post a picture of that box?

wiring

Ok the red and black wires runs to the front of the boat somewhere to most likely to the key switch on the box it says ignition protection 20 amp 24 volt DC so what I'm thinking is a small red and black wires would run to the house battery hey feed all the interior lights radio fish finder all that stuff I'm putting the combiner 100 on. I'm working on putting a picture

A little side humor since I bought the boat 3 weeks ago It has been bad weather in Dallas every weekend I guess the joke is on me Thanks for everyone's help

if you want the wind to die down, just buy a sail boat

Yeah all week long it has been gorgeous weather And on Friday they start talking high winds and rain

wiring

these is the wires

wiring

one more pic of the red and black wire