Your problem may be more than using some exterior wood filler. What stands out to me is that there is no gutter above that section of windows and water is pouring onto your lower roof and those lower boards are just soaking it up and causing the damage u describe.
Have a proper gutter installed above before u do anything.
Next u may have rotting wood behind the boards u see..like plywood etc..
Any rotting wood i wood remove and replace.
But first address the main issue which is the lack of a proper gutter on your home. That's my 2 cents. Good luck. Also, having a proper gutter installed by a pro should be fairly cheap...