They make paintable wood filler for just these situations. It's easy to sand down, has good durability and can be painted over for added protection. Try to find some that doesn't shrink when it dries.
There is a product called Arbitron that is design for this purpose...problem is, with putty it is essential that you get all of the rot out FIRST before patching. Much better off to replace/repair the rotted pieces and back-prime all of the wood.
They make paintable wood filler for just these situations. It's easy to sand down, has good durability and can be painted over for added protection. Try to find some that doesn't shrink when it dries.