I always paint after application...
"...you can use Durham’s Water Putty outdoors. Our material will withstand the weather when used outdoors, but it must be kept painted.
"Water putty is not waterproof, and if it is exposed to moisture, that moisture will be absorbed by the putty and the paint can peel from damp putty patches. If you see any peeling of the paint on a putty patch, you need to find the source of the moisture and correct it so that the moisture is not getting to the putty.
"Be sure not to spread the putty in a thin layer over a flat surface, since the putty is intended to be put INTO holes or cracks or voids and not just applied over the surface of a board. When the putty is put over the flat surface of a board, it can come loose when the board expands and contracts during changes in the weather.
"If you have a very deep void that you are filling (such as from rot or something) fill it in about 1/4 inch layers, allowing it to dry overnight between layers. That way, the moisture will have a chance to dry out well between applications, and the patched area will be better prepared and have a lower moisture content when you paint it.
Bondo type fillers will work as well...